Re: 13C relaxation Model-free

[Edward d'Auvergne]

On 3 April 2017 at 16:02, Troels Emtekær Linnet  wrote:
> Hi Sahil.
>
> Try the tutorials listed here:
>
> http://wiki.nmr-relax.com/Category:Tutorials
> http://wiki.nmr-relax.com/Tutorial_for_the_relaxation_dispersion_auto-analysis_in_the_GUI
> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi
> http://wiki.nmr-relax.com/Manual
>
> I can get access to the wiki on my chrome, so it should work.
>
> Note, most of the tutorials has been written to the dataformat of Varian.
> And some of the tutorials has been written to a more "general" dataformat.
>
>
> If you have problems with getting the tutorials to work, I could write a
> new tutorial for you.
>
> That would need:
> * An overview of experiments, which field strength, etc.
> * Some sample files with the format. You can limit the amount of data to
> 1-2 spins, to keep confidentiality.

Hi Sahil,

Have you been able to work out how to use the relax GUI for your data?
 Do you have multiple field strength data?  Is this data for a pure
dipole system, or do you have multipole relaxation present?  Note that
the relax trunk does not handle multipole relaxation at the moment.

Regards,

Edward

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Re: S^2 differences between proteins

[Edward d'Auvergne]

On 3 March 2017 at 19:51, Mahdi, Sam  wrote:
> Hello everyone,
>
> This isn't as much a problem with relax as it is a general question
> regarding S^2 values itself. When comparing different values of S^2 between
> proteins, what difference is considered significant. Due to the lower
> values I know say an average S^2 value of .1 is a big difference in the
> flexibility of one protein to another, but what about say an average
> difference of .01, is that still considered a significant change in
> considering the relative dynamics of one protein to another? (I.e. if say,
> protein A has an average S^2 value of 9, and protein B has an average S^2
> value of 8.9, could you make the statement Protein A has significant
> dynamic differences, more rigid, when compared to Protein B. Or could you
> make the statement due to only a difference of .01, there isn't much of a
> overall dynamic difference between the 2 proteins)?

Hi Sam,

Sorry for not getting back to you earlier, I have been extremely busy
lately!  This is really a statistical problem.  And it depends on the
quality of your parameter error estimates.  If you have two values and
two associated errors, then you can look at hypothesis testing / ANOVA
statistics to tell you if the two values are statistically different
(i.e. 1st year Uni stats).  Note that your error estimates should
include the variability of the diffusion tensor, as that will account
for probably around 80% of the influence on the relaxation data, and
without this variability a S2 parameter comparison is meaningless.
There is no rule for S2 differences so you need to rely on basic
statistical tests.

Regards,

Edward

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Re: Relax app MacOS run script

[Edward d'Auvergne]

On 21 April 2017 at 11:02, Pavel Macek  wrote:
> Hi Edward,
> I have issues running the relax script from terminal on MacOs.
>
> I installed relax using the downoladed dmg instaler relax-4.0.3.Darwin.dmg.
> 
> In principle the relax works, although I face some issues loading the peak
> intensities relaxation dispersion. Here when I select the file it is not
> displayed in the "The file name(s)" field unless I press the "nagnifying
> glass" icon in the read file pop-up window.

Hi Pavel,

For this issue, could you please create a bug report at
https://gna.org/bugs/?func=additem&group=relax ?  That will hopefully
help me replicate the issue, assuming it is not dependent on the OS X
version, and then fix it.  It however sounds like a bug in wxPython.

Cheers,

Edward

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Re: Relax app MacOS run script

[Edward d'Auvergne]

On 24 April 2017 at 20:28, Troels Emtekær Linnet  wrote:
> Dear Pavel.
>
> Welcome to the relax mailing list.
>
> For the .dmg installation, it is only possible to use the GUI.
>
> But you can install relax another way.
>
> Have a look here.
> http://wiki.nmr-relax.com/Category:Installation

Hi,

Let me add that after launching the relax GUI from the Mac App, you
can run scripts directly from the 'User functions->script' menu.  Mac
Apps are designed to be GUI only ;)  If you want to be a power user
and use the command line directly, then you need to follow Troels'
advice.  Troels has created awesomely detailed resources on the relax
wiki for this.

Regards,

Edward

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Re: Error in model free analysis

[Edward d'Auvergne]

Hi Ashish,

I had a look at the results file, and I think the problem is that you
are loading a corrupted PDB file format.  The Z coordinates for all
atoms is set to None!  You can see this at the bottom of the file.
The first few coordinates are:


[-14.56, -14.35, -12.87, -12.01, -14.73, -16.17, ...
[snip]


[6.0, 2.0, 9.0, 1.0, 5.0, 7.0, ...
[snip]


[None, None, None, None, None, None, ...


Because of the strange coordinates, especially integers for the Y
coordinate and nothing for the Z, this can only be an incorrectly
formatted PDB file.  Note that the character position is what counts
in the PDB format.  Could this be the reason?

Regards,

Edward



On 22 February 2017 at 12:01, Ashish Sethi  wrote:
> Hi Troels,
>
>
>
> I am having troubles login to my account. So I have uploaded the results.bz2 
> file on my drop box and this is the link to it:
>
>
> https://www.dropbox.com/s/86teapt1isbo8zr/results.bz2?dl=0
>
>
>
> Hope this helps to access the files.
>
>
> Thanks
>
>
> Ashish
>
> 
> From: tlin...@gmail.com  on behalf of Troels Emtekær 
> Linnet 
> Sent: Wednesday, February 22, 2017 8:02:24 PM
> To: Ashish Sethi
> Cc: relax-users@gna.org
> Subject: Re: Error in model free analysis
>
> Hi Ashish.
>
> Attachments to the mailserver is dropped.
> Can you provide a bug report instead, at upload the file there?
>
> https://gna.org/bugs/?func=additem&group=relax
>
> Best
> Troels
>
> 2017-02-22 8:56 GMT+01:00 Ashish Sethi 
> mailto:ashish.se...@unimelb.edu.au>>:
> Dear Edward,
>
>
>
> I also tried running the same calculation on my personal macbook pro (OSx EI 
> Capitan) and I got the following errors:
>
>
> relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model 
> free LDLamodule/local_tm/aic')
>
> Opening the file '/Users/ashishsethi/Desktop/model free 
> LDLamodule/local_tm/aic/results.bz2' for reading.
>
> Exception raised in thread.
>
>
> Traceback (most recent call last):
>
>   File "gui/analyses/execute.pyc", line 87, in run
>
>   File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute
>
>   File "prompt/uf_objects.pyc", line 225, in __call__
>
>   File "pipe_control/results.pyc", line 97, in read
>
>   File "data_store/__init__.pyc", line 512, in from_xml
>
>   File "data_store/pipe_container.pyc", line 244, in from_xml
>
>   File "lib/structure/internal/object.pyc", line 1714, in from_xml
>
>   File "lib/structure/internal/models.pyc", line 155, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 632, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 449, in from_xml
>
>   File "lib/xml.pyc", line 287, in xml_to_object
>
>   File "lib/float.pyc", line 200, in packBytesAsPyFloat
>
> error: pack expected 8 items for packing (got 571)
>
>
>
> I have attached the results.bz2 file with this email.
>
>
>
> Thanks
>
>
> Ashish
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Re: Error in setting up model free analysis

[Edward d'Auvergne]

On 21 February 2017 at 07:29, Ashish Sethi  wrote:
> Thanks Sam.
>
>
>
> I did ignore the error message and run the model free analysis and I got the 
> following errors:
>
>
>
> Traceback (most recent call last):
>   File "/usr/local/relax/gui/analyses/execute.py", line 87, in run
> self.run_analysis()
>   File "/usr/local/relax/gui/analyses/auto_model_free.py", line 808, in 
> run_analysis
> dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, 
> pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, 
> diff_model=self.data.global_models, mf_models=self.data.mf_models, 
> local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, 
> diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, 
> mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, 
> conv_loop=self.data.conv_loop)
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in 
> __init__
> self.execute()
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in 
> execute
> self.interpreter.results.read(file='results', 
> dir=self.results_dir+'local_tm'+sep+'aic')
>   File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__
> self._backend(*new_args, **uf_kargs)
>   File "/usr/local/relax/generic_fns/results.py", line 96, in read
> ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
>   File "/usr/local/relax/data/__init__.py", line 452, in from_xml
> self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
>   File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml
> self.structure.from_xml(str_nodes[0], dir=dir, id=parser, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in 
> from_xml
> self.structural_data.from_xml(model_nodes, id=id, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in 
> from_xml
> self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in 
> from_xml
> self[-1].from_xml(mol_node, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in 
> from_xml
> xml_to_object(mol_node, self, file_version=file_version)
>   File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object
> value[i] = packBytesAsPyFloat(ieee_value[i])
>   File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat
> doubleString=pack('8B',*bytes)
> error: pack expected 8 items for packing (got 571)
>
>
>
> Can anyone suggest what is the problem ?

Hi Ashish,

Such an error message means that the relax results file is corrupted
somehow.  Maybe check that you haven't run out of hard disk space or
that there are no bad sectors on the hard disk.  You could also open
up the results_dir+local_tm/aic/results.bz2 file and see if that file
looks ok.  If there is nothing wrong with your hard disk, could you
open up a bug report at https://gna.org/bugs/?func=additem&group=relax
and attach the results.bz2 file causing the problem?  If you'd like to
keep your data private, try deleting residues from the XML file until
you only have 1 or 2 left, and use the state.load user function to
make sure that that exact "error: pack expected 8 items for packing
(got 571)" message is still present.

Regards,

Edward

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Re: Error in setting up model free analysis

[Edward d'Auvergne]

On 21 February 2017 at 05:40, Ashish Sethi  wrote:
> Dear Edward,
>
>
> Hope this email finds you well !!!
>
>
>
> I am a beginner in the field of protein dynamics and I wish to do a model 
> free analysis for my protein which is about 72 residues (8.5 kDa). I have 
> calculated the standard R1, R2 and NOE (steady state) parameters and also did 
> the reduced spectral density mapping.
>
>
> My question is related to dipolar relaxation settings while setting up the 
> model free analysis, so all my files (R1, R2 and NOE) only have 15N spin 
> information and if I follow the instructions given in the manual and select 
> "@N" and "@H"-- i get an error saying no information available for H spin 
> which is obvious. In this case what am I supposed to select ? Apologies for 
> my naivety.

Hi Ashish,

Welcome to the relax mailing lists!  Note for a model-free analysis
that for over 2 decades now it is expected that you collect data at 2
or more field strengths.  I suggest you have a read of the following
reference to understand why a model-free analysis fails - i.e. you end
up with artificial Rex and nanosecond motions:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494.  (http://dx.doi.org/10.1039/b702202f).

As for the error, this should actually be a RelaxWarning saying that
the H spins are deselected as there is no relaxation data.  If you
have a RelaxError, or any other Python Error, could you copy and paste
that error message?  Otherwise, the RelaxWarning is what you should
expect.

Regards,

Edward

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Re: (relax:22417) GVFS-RemoteVolumeMonitor-WARNING

[Edward d'Auvergne]

On 16 January 2017 at 21:50, Xu, Shenyuan  wrote:
> Dear relax managers,
>
> I installed the relax based on the installation guide on "installation
> linux".
>
> When I run the full test suite command, it shows the "relax:22417
> GVFS-RemoteVolumeMonitor-WARNING". Then I opened the log file, it said
> system/funtional testsfailed
> unit testsok
> gui tests-ok
> software verification testsfailed
> synopsis-failed.
>
> Then I run a R1 analysis on the gui mode and after three days, relax shut
> down itself and on the terminal, it said: "mpirun noticed that process rank
> 0 with PID 28252 on node tetra exited on signal 9 (Killed)".
>
> What should I do?
>
> I really appreciate your help!

Nihao Shen!

Welcome to the relax mailing lists.  For the error you see, which
version of relax are you using and which operating system (and
version) are you using?  For bugs, I would recommend creating a bug
report at https://gna.org/bugs/?group=relax and attaching log files
there.  For example the full log file from test suite would be very
useful to see what is happening.  Note that you cannot attach large
files to a mailing list post - this is blocked to avoid a large strain
on the infrastructure.

Also, I don't know how stable OpenMPI is when running through the GUI,
but that mpirun shutdown notice sounds like the GUI was killed by the
operating system for some unknown reason (likely outside of relax's
control).  Hopefully that wouldn't happen on a second run.
Alternatively, you could try the prompt/script UI mode to see if the
GUI is the issue.

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 15 November 2016 at 14:33, Jeremy Anderson  wrote:
> Hi Edward,
>
> Thanks for the follow up.  I totally understand the reasons for not having
> fixed values within a relax analysis, it seems like a special case relative
> to what I've seen in the literature and increases ones ability to skew the
> results to their liking, I'm doing my best to safeguard against that myself.

No problems.  You do have to be quite careful, as it is far too easy
to fall into an alternative reality that can nicely explain some of
the biology.  Mapping the optimisation space is an essential tool when
constraining certain parameters to see if you are at a well defined
minimum.  For example it can show you if you've just chopped across a
valley in the space and the optimiser is landing at the bottom of that
valley where it has been cut.  If you have access to the ancient, yet
very powerful OpenDX software, you can use the dx.map and dx.execute
relax user functions for this.


> I was able to implement such an analysis in python using the RD models from
> relax as well as the scipy and lmfit packages to both hold the dw parameters
> constant while performing the usual grid search then nonlinear least squares
> minimization and perform a cluster analysis holding the rate constant and/or
> the major population constant amongst all residues.  The code is a bit of a
> mess at the moment but I'm hoping to clean it up and make a repository on
> github, so I can better document what I did and so other folks can check it
> out if they want.

Note that I originally looked at the scipy optimisation packages for
relax.  However I found fatal bugs in all three of the algorithms
implemented at the time (Levenberg-Marquardt being one of them).  The
algorithms appeared to minimise the results, but they were nothing
like what Art Palmer's Modelfree4 found.  I was comparing relax to
Modelfree4 for debugging at the time when implementing the model-free
analysis component.  I don't know if anything has changed since then,
but you really need to be wary and double check whenever you use any
part of scipy.  Anyway, because scipy's optimisation was so terrible,
I decided to write the minfx optimisation library
(https://gna.org/projects/minfx/).  You'll see a record of all of this
in my publication history ;)


> Thanks for your assistance.

You're welcome!

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 27 October 2016 at 18:10, Jeremy Anderson  wrote:
> Hi Edward and Troels,
>
> Thanks for pointing me in the right direction.  I had dug around a bit in
> the test_suite directory but wanted to make sure I was looking in the right
> place before I descended into the rabbit hole.
>
> I got the back calculation to work using the
> ./test_suite/shared_data/dispersion/ns_mmq_3site_linear/relax_results/solution.py
> script pretty much as-is, just changing the spin parameters to my liking,
> calculating the curve, and outputting the values (ignoring the data and
> residuals in the output file).
>
> Something I didn't mention is that the reason I've been importing the models
> into ipython is so I can hold parameters constant through my own grid search
> and minimization functions, which I had found somewhere in the documentation
> was not possible inside relax for the minimization.  I originally thought
> this would be easier outside of relax.
>
> The reason for this is because I'm in a situation where I can observe HSQC
> peaks in slow exchange in one variant and skewed populations of one or the
> other peaks in two other variants.  I've been working on using the
> complementary information, in this case the observed dw and the kex from ZZ
> exchange experiments, to investigate multi-state exchange in all variants.
>
> The chem. shift differences of the two skewed variants match the measured
> nicely but the rates from CPMG are ~20 fold higher.  Therefore I wanted to
> check and see if a 3-state model with some parameters held constant would
> have infinite solutions (my assumption) or pop out something interesting and
> be able to distinguish between a couple models of the conformational process
> that I have in mind, which seems like a long shot.
>
> Sorry if thats too much information/way too open-ended but I figured I would
> give some context to the greater situation I have found myself in.  Thanks
> again!

Hi Jeremy,

It is true that you cannot fix a parameter in relax and optimise the
others.  The reason is two-fold.  Firstly the minfx library (
https://gna.org/projects/minfx/ ) does support this functionality.
Secondly, this functionality would be highly abused and a lot of
rubbish results will appear in the scientific literature, with a
detrimental effect on the reputation of the whole NMR field.

Also, I didn't think it was worth the time investment compared to
expanding relax to handle multiple data types at the same time, and
then optimising one set of parameters for all experimental data
simultaneously.  In your case, that would be loading the ZZ exchange
and CPMG data at the same time, and optimising the single model.  This
would be interesting, as the two experiment types contain both
complementary and overlapping information content.  So saying that the
overlapping content should only come from the ZZ experiment might
over-constrain the CPMG experiment due to any biases or experimental
noise from that experiment.  Are you able to set up the problem in
this alternative way in iPython?

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 29 October 2016 at 23:44, Mahdi, Sam  wrote:
> Hi Edward,
>
> I was reading the theory on model free within the manual and I had a quick
> question. The d'Auvergne protocol, is that the model-free analysis in
> reverse with the universal solution?

Yes, that is the technique.

> Or is that the model-free models with
> only the AIC model selection (no universal solution). Both methods were
> under the new-protocol section, so I was confused a bit as to which one the
> d'Auvergne protocol is running.

This is a fragment of the protocol.  It is one part of the iterative
procedure shared with the methods that require an initial, external
diffusion tensor estimate.  The key references to understand all of
this are:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133.
(http://dx.doi.org/10.1007/s10858-007-9213-3)

Regards,

Edward

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Re: Using modified all models free

[Edward d'Auvergne]

On 1 November 2016 at 22:12, Mahdi, Sam  wrote:
> Hello everyone,
>
> I had a quick question regarding running the single model free run (m4).
> For some proteins we only have data at only one field strength, so I know I
> can't use the d'Auvergene protocol (needs a minimum of 4), so I was
> thinking I could run the all models free model. The problem is, I know
> models m6-m9 are models for another field strength, but since I don't have
> data at another field strength, could I just remove them? Or will relax
> just not run m6-9 since I've only loaded one field strength?

Hi Sam,

The protocol I designed for iteratively optimising and fine tuning the
coupled diffusion tensor + model-free optimisation and model selection
problem will only work with 2 or more fields.  If you would like to
understand this problem, please read:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

From this, hopefully you will understand why the NMR field will not
take any results from a single field strength analysis seriously.
Note that this has been the case since the mid 1990's.

Regards,

Edward

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Re: Using Model-free models

[Edward d'Auvergne]

On 10 November 2016 at 23:50, Mahdi, Sam  wrote:
> Hello everyone,
>
> I've been attempting to run model free models (due to only have data at one
> field strength), but I've come across a problem. I have set up both the
> model free models script and the model free model selection, both models
> run fine, and I do end up receiving data that does make sense and is good;
> however, the script doesn't seem to actually select any models. I.e. if I
> put in the m0-m9 in the script, it'll select m9 for every single reside and
> only give me Rex data and no S^2. If I run m0-m4 same thing, it'll run
> every residue at m4, instead of running through all the models and
> selecting the data that fits that model. I know it states that the model is
> supposed to loop through every model, then you run the model selection to
> select what model fits which data set, but I don't know if my script is set
> up incorrectly or what. Here is my script for model-free models:
> pipes = ['m0','m1','m2','m3','m4']
> for name in pipes:
> pipe.create(name,'mf')
> sequence.read('ssNOE_RGS4Agnes',res_num_col=1)
> spin.name('N')
> spin.element(element='N',spin_id='@N')
> spin.isotope('15N',spin_id='@N')
> structure.read_pdb('cluster1_12.pdb',read_mol=1)
> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
> file='R1_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
> file='R2_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
> file='ssNOE_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
> diffusion_tensor.init(1e-8,fixed=True)
> sequence.attach_protons()
> interatom.define(spin_id1='@N',spin_id2='@H',direct_bond=True)
> interatom.set_dist(spin_id1='@N',spin_id2='@H',ave_dist=1.02*1e-10)
> structure.get_pos('@N')
> structure.get_pos('@H')
> interatom.unit_vectors()
> value.set(-172*1e-6,'csa',spin_id='@N')
> model_free.select_model(model=name)
> minimise.grid_search(inc=11)
> minimise.execute('newton')
> results.write(file='results',force=True)
> state.save('save',force=True)
>
> Again I only have it at m0-m4 because I wanted to obtain the m4 data, but
> even if it is to m9, it'll only run the m9 model (i.e. I will only receive
> Rex data because that's whats attributed to m9).  Here is my model
> selection script:
> pipes = ['m0','m1','m2','m3','m4']
> for name in pipes:
> print("\n\n#"+name+"#")
> pipe.create(name,'mf')
> results.read(file='results.bz2',dir=name)
> eliminate()
> model_selection(method='AIC',modsel_pipe='aic')
> state.save('save',force=True)
> results.write(file='results',force=True)
>
> Again, this is only set up to m4 for the same reasons as before. I don't
> know whether or not I have something in my script set up, but my final
> results file just shows the model that was selected for every residue, is
> the last model I have in my pipes (i.e. if m4 is the last model, it'll run
> model 4, if m9 is the last one, it'll run m9). In this sence it appears to
> be a single model scenario even though I've set up to be for multiple
> models. Thank you again in advance.

Hi Sam,

This is perfectly normal!  The key is the line:

diffusion_tensor.init(1e-8,fixed=True)

Here you have fixed the diffusion tensor to spherical tumbling of 10
ns.  Note that >80% of the contribution to relaxation is due to the
global tumbling.  So if you get this global tumbling wrong, it has an
absolute crushing effect on the remaining 20% and the fine model-free
parameter values and model selection dependent on that 20%.  So
obtaining a very good estimate for the molecular Brownian diffusion is
essential, otherwise you should expect catastrophic failures in the
fine internal motions (which is what you are seeing).  This is why in
the last 20 years, that no one will take any published results
seriously if you do not have data at two field strengths.  It is also
why I developed that long protocol for obtaining a highly refined
diffusion tensor together with the internal motions.

You may think that you can obtain a diffusion estimate from another
technique (optical rotation data, hydrodynamics bead modelling, MD
simulation, etc.), however these are either not good enough or plain
wrong, specifically because of the packing interactions and
microviscosity in your NMR tube being poorly, or not at all, modelled.
It is imperative that the diffusion tensor is optimised against the
relaxation data.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 4 October 2016 at 23:23, Mahdi, Sam  wrote:
> Hi Edward,
>
> Just wanted to update you on the status of my runs. I had 2 potential dimer
> structures. I ran Chain A and B for one of them, and Chain B for the other.
> All the results were all very similar. There was missing data though
> throughout (i.e. I had data for some residues for Chain A that had no data
> in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
> would have data, but Chain B for the other pdb file wouldn't). The data that
> is there for all 3 though does make sense. Thank you so much for your help

You're welcome!  Thanks too to Troels and Gary for answering most of
your questions.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 10 October 2016 at 23:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> Wanted to update you a prior problem I had. So I ran relax with multiple
> processors and single processor with the same data set, and obtained
> identical data on my computer. So the previous issue I had with missing data
> I don't think is related to relax itself. Just wanted to let you know.

This is great to hear.  The relax test suite is a gold standard which
shows that this should always be the case.  Though there are a few
extremely minor differences when using different operating systems and
32 vs. 64-bit systems, the code paths for running on the multi and
uni-processors is identical.  This is thanks to Gary Thompson's great
design of the multi-processor system :)

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 21 October 2016 at 00:14, Jeremy Anderson  wrote:
> Hello,
>
> I've been trying to back calculate data from parameters using the NS MMQ
> 3-site linear model.  I've tried to do something akin to the
> sample_scripts/model_free/generate_ri.py sample script as described in the
> mail-archive .
> I'm afraid that I'm not knowledgable enough about the data structures,
> parameters, and functions of relax.
>
> Up to this point I have been simulating data using the CR72 and TSMFK01
> dispersion models by importing the R2eff functionality of each module into
> an ipython notebook and supplying parameters interactively.  I've attempted
> this with the NS MMQ 3-site linear model however I'm getting lost in the
> structures of the input parameters.
>
> Ideally what I would like to be able to do is input the parameters:
>
>
> pA, pB, pC = .8, .15, .05
>
> R20A, R20B, R20C = 10, 15, 20 (s^-1)
>
> dw_AB, dw_BC = 2, 2 (ppm)
>
> kex_AB, kex_BC, kex_AC = 400, 200, 0 (s^-1)
>
> dwH_AB, dwH_BC = .2, .2 (ppm)
>
>
> into the r2eff_ns_mmq_3site_mq and/or r2eff_ns_mmq_3site_sq_dq_zq functions
> of the ns_mmq_3site module and populate a back_calc array with R2eff
> values for nu_cpmg = np.logspace(1, 3, 20).  I've done the same with the
> 2-site models I mentioned above but I feel I'm a bit over my head here.
>
> Any help would be greatly appreciated and thanks in advance *and* bravo for
> all the work on relax, its great!

Hi Jeremy,

Welcome to the relax mailing lists!  I was wondering if you were able
to work out what to do from Troels' comment?  He has written a lot of
such data back-calculation scripts which can be found in the
test_suite directories, and if you look for scripts and data in there,
you should hopefully be able to see what to do.  As for all the work,
this is a community project with many contributors:

http://gna.org/project/memberlist.php?group=relax

For example Troels has put a lot of work into the relaxation
dispersion analysis, adding many models and making this part super
fast:

http://wiki.nmr-relax.com/Relax_release_descriptions#relax_3.3.0

Hopefully you'll be able to use relax for your purposes and, if not,
maybe you'll be able to expand relax and contribute a little yourself
;)

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 5 October 2016 at 22:01, Mahdi, Sam  wrote:
> Hi Troels,
>
> The mpirun --np 2 gave no output, so I had to abort the command, but here is
> the output.
> crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> 1.3.1
> crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> MPI.COMM_WORLD.Get_rank()"
> ^Ccrowlab: [~]>

Hi Sam,

This result I'm pretty sure shows that mpi4py is not functioning
correctly - i.e. there is an installation problem.  This is what you
should see:

[edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
print MPI.COMM_WORLD.Get_rank()"
0
1
[edward@localhost ~]$

Note the printout of 0 and 1.  Maybe try the following:

[edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
%(mpi4py.__version__,
MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
MPI.Get_processor_name()))"
Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
[edward@localhost ~]$

If you don't see a printout here, then clearly mpi4py and OpenMPI are
not working together correctly.  Without a printout, your mpi4py is
FUBAR.  Are you using the default OpenMPI and mpi4py packages form
fedora, and you don't have any backports or other non-standard sources
set up for your RPMs?  Do you have any user installed MPI or mpi4py
software around?  If you type:

$ locate mpi

What do you see?  For me this is pretty clearly an installation problem.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 1 October 2016 at 20:14, Mahdi, Sam  wrote:
> Hi Edward,
>
> Oh ok. Thank you for your help, I was able to resolve the problems I had
> with both proteins, and now they are both running. Since there is symmetry
> within the dimer, both chain A and chain B will give me the same S^2 results
> correct?

Hi Sam,

That depends.  If you superimpose A and B and have an RMSD of
0.0, then the S2 values will be identical.  But if
the docking software changed the monomer structures slightly so the
RMSD is not exactly zero, then the S2 values will be slightly
different for some residues.  You can use relax to superimpose
structures and determine the RMSD to very high precision, if you like,
but I'll leave that to you as a learning exercise ;)

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 23:42, Mahdi, Sam  wrote:
> Hi Edward,
>
> So when I ran it as read_mol=0, it gave me the same error. But it worked
> once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1 was
> for set B?

Sorry, I just remembered that the molecule numbering starts from 1.
So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
should add a check for this argument.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 19:45, Mahdi, Sam  wrote:
> Sorry, I just want to make sure I fully understand this so I can explain it
> to my PI:

No problems, this is by far the most complicated aspect in the field of NMR ;)


> So if there is symmetry, I can upload the same pdb file with the dimer (set
> A and B) but tell it to read only one set.

Load rather than upload, but yes.


> Since S^2 isn't effected too much
> versus a dimer versus a monomer, the only thing that is important is the
> change in co-ordinates of one set of the dimer (i.e. the differnence in
> co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
> or set A in a different version of that dimer's co-ordinates).

S2 is not affected by the reference frame.  This only matters for
comparing diffusion tensors.  Though you will only ever see one
tensor, as that is what is in your NMR sample (if you have a
monomer-dimer mix, then you're in trouble and will see a lot of
artificial Rex and ns motions).


> I say this
> because I have already run my protein's data with the pdb structure of the
> monomer, and I have 2 different pdb files the docking program gave back for
> the dimer (2 different ways the dimer could form from one interface).

Well, your analysis will always return the same diffusion tensor.  If
you want these diffusion tensors to all be in the same frame, use the
relax structure.superimpose user function with the method='fit to
first' argument.  Then just pick which will be your reference
structure and superimpose.  You can superimpose A and B - separately -
onto the monomer frame.

Let's pick the monomer as the reference frame.  Then:

- If you superimpose "dimer 1, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 1, struct B" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct B" to the monomer, you
should find the same tensor.

If the docking program did not optimise the internal monomer
structure, you will get identical results.  Otherwise you'll see minor
internal motion changes.  If your PI was hoping that you would be able
to tell him that you have a monomer or one of the 2 dimers in your NMR
tube, well then you will need to start to read many, many papers on
diffusion tensor prediction.  But know that all prediction methods
underestimate the diffusion tensor (e.g. David Case is working on this
exact problem for MD simulations).  In this case, relaxation data is
not the best NMR method for this.  It would be better to use RDCs from
a purely steric alignment and to compare that to what PALES prediction
comes up with (though that itself is still a very rough and imperfect
method).

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:47, Mahdi, Sam  wrote:
> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.

The reason is because either OpenMPI or mpi4py are not working.  If
you compiled OpenMPI, then you'll have to compile mpi4py against that
self-compiled version of MPI.  Having multiple versions of MPI on the
system might be problematic, unless you know how to set your
environmental variables correctly for compilation and linking.  If you
cannot run the mpi4py demo that comes with the mpi4py source code,
then you do not have it set up correctly.  If you need help setting up
mpi4py for Python, please see the "Discussion and Support" section at
https://pythonhosted.org/mpi4py/ .  I don't think anyone on the relax
mailing lists have experience with broken mpi4py installations and can
help you fix this.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

Hi Sam,

Please see below:

> I'm a bit confused to that. If the protein is a dimer, and the tumbling
> decreases, will that not results in altered  relaxation data?

Yes.

> Won't the
> relaxation data average be higher, since it is relaxing slower due to its
> increased size (tumbler slower in solution=slower relaxation back to
> equilibrium)?

No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
affected too much, but it may decrease (maybe).  You need to
understand how the diffusion tensor affects the J(w) spectral density
curves to understand how R1 and the NOE will be affected.


> Also, doesn't S^2 take into account the overall shape of the
> molecule (as well as tensor type) in it's calculations?

No.  The S2 value is the internal motions of the residue.  It is 100%
independent of the global tumbling.


> So won't a dimer
> versus a monomer change the results just due to that?

Not at all.  The optimised diffusion tensor should change, and the S2
value stay the same.


> So should I input both, read_mol=0 and read_mol=1?

No, only one.  You can, however, perform a second analysis later with
read_mol=1 (for comparison).


> So
> structure.read_pdb(file='cluster1_12.pdb', dir=None,
>  read_mol=None, set_mol_name='hRGS4',
> read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
> merge=False)
> So mol_num=0 will be for chain A and mol_num=1 for chain B?

This will have the same IndexError as before - relax will not handle
two identical molecules in a model-free analysis at the same time.
Again, this theory simply does not exist.  So I haven't added it to
relax.  You need to perform the analysis on a single monomer of the
homodimer.  But please check for symmetry - if you don't have
symmetry, nobody on the planet can currently analyse non-symmetric
homodimer data.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> So I ran the the mpirun commands you suggested. The echo world works fine. I
> get the same results you did. For the relax one, this is the output I
> recieved
>  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> Usage: relax [options] [script_file]
>
> RelaxError: incorrect number of arguments

Have a close look at my original text:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

Note how "relax 4.0.2" is on a different line - that is the relax
output, not the command line input.  Try again without that text.


> RelaxError: ambiguous option: --v (--verification-tests, --version?)

This is because the double-dash to single-dash conversion is only in
the HTML version of the relax manual, and not emails.  Run "relax -h"
to see a description of this option.


> Also, the reason its ./relax is because I have relax 2.2.5 installed, and I
> have that set up as an Alias, so if I just type relax, it'll open up relax
> 2.2.5. So I went to the actual relax-4.0.2. directory instead of indicating
> its path and just typed ./relax. (By I, I mean the administrator of this
> computer, I do not have root access to this computer).

You should set your alias to the relax-4.0.2 version instead.  The
2.2.5 version is very, very old, and many bugs have been fixed since
then.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:03, Mahdi, Sam  wrote:
> Hi Edward,
>
> So the GUI problems came from relax 2.2.5 The actual output is big, so I
> will only post where the errors started
> relax> monte_carlo.error_analysis()
>
> relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
> force=True)
> Opening the null device file for writing.
> Traceback (most recent call last):

[snip]

> "/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
> line 121, in 
> print("A:\n" % cdp.align_tensors[0])
> TypeError: not all arguments converted during string formatting

[snip]

> That was for relax 2.2.5

These issues were fixed a long, long time ago ;)


> This is the output for relax 4.0.2 It seemed to run and finish, but it gave
> a bunch of errors that stated
> (python:28738): IBUS-WARNING **: Create input context failed: Timeout was
> reached.
>
> This warning basically takes up the entire terminal. Followed by this

These issues are with your Ibus input system, which I guess you have
set up for a few Indian languages on top of English, interacting with
wxPython (again a Fedora configuration issue).  Those are wxPython
messages which are not related to relax.  You should run the wxPython
demos and see if you can type with different Ibus languages, and see
if you get these same Ibus warnings.  No need to report back here
about that though - it would be of more benefit to report this
upstream to Fedora.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 17:37, Mahdi, Sam  wrote:
> Hi Edward,
>
> I also wanted to add, for running a multi-processor platform problem. I
> installed openmpi from the fedora package list, not from the site itself. I
> installed both openmpi, mpi4py, and the openmpi devel. I did not modify
> anything. I can also successfully open relax using mpirun in a single
> processor mode (as in I can load the module, and do mpirun relax and it'll
> work). Do I actually have to do some modifications to openmpi for relax? The
> other computer I was able to successfully run multi-processor on, already
> had openmpi installed and set up, so I only downloaded mpi4py on that
> computer. So I don't know what their setting or configuration was.

Hi Sam,

This sounds like a Fedora OpenMPI misconfiguration.  I guess on the
computer that you see no output with relax, you would also see no
output with:

[edward@localhost ~]$ mpirun -np 5 echo "hello"
hello
hello
hello
hello
hello
[edward@localhost ~]$

In any case, this has nothing to do with relax.  And without a local
login to your computer, there is not much anyone can do about it.  Do
you have a system administrator there who can help you?  Oh, another
good and quick test is:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

You should only see a single version number printed.  This tests both
your OpenMPI configuration and the mpi4py Python package.  If you do
not see these exact same results, you have some configuration work in
front of you ;)

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 17:31, Mahdi, Sam  wrote:
> Hi Gary,
>
> There is only a monomer version of it on pdb, so if you mean it in that
> sense, yes. I obtained results from it; however the S^2 were very high, but
> I attributed this to having data for a dimer, but using a monomer pdb file.

Hi Sam,

This cannot be the case.  The S2 values are often very similar in a
monomer and homodimer case.  Or a trimer, tetramer, etc.  The only
difference is that the global tumbling - the diffusion tensor - is
slower in the dimer/trimer/tetramer/etc. (and the tensor type and
shape will be different due to the different hydrodynamic+water shell
shape).


> If you mean have I tried to just delete set B from the pdb file I uploaded,
> I have not attempted that.

With relax, you should never modify the PDB files - relax can do that
for you much better and to the PDB standard via the PDB user
functions.


> So I am a bit confused here, so if I add read_mol=1 instead of my
> read_mol=0, it'll only read set A?

Sorry, I meant "read_mol=0" for PDB chain ID A.  The argument
read_mol=1 will pull out chain ID B.


> Assuming symmetry, relax will
> automatically calculate and determine set B?

Assuming symmetry, you will get the identical results for read_mol=0
and read_mol=1.  There might be slight differences in bond orientation
if the symmetry is not perfect.

If there is no symmetry, the relaxation data for monomer A and monomer
B will be different, but it will be averaged to a single value.  If
this is the case, as I said before there is no theory on the planet
for properly handling such averaged data, and you cannot perform any
model-free, reduced spectral density mapping (J(w) mapping), or other
analysis on it.

I hope this clarifies the situation a little better.

Regards,

Edward

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Re: Issue in ModelFree Calculation

[Edward d'Auvergne]

On 26 August 2016 at 18:25,   wrote:
> Hi Edward,
> Thank you for your suggestions. Extremely sorry for my late reply. I already
> tried what Troel had told me. As I didn't install the SciPy package (not
> required for ModelFree analysis), I am unable to perform the full test
> suite. As per your suggestion, I went through the wxPython demo, and found a
> missing link of a library package which I have successfully rebuild. Now
> wxPython is setup correctly. But still I get the same error like previous:
>
> terminate called after throwing an instance of 'std::bad_alloc'
>   what():  std::bad_alloc
> Abort (core dumped)
>
> This time I didn't get errors with the libraries. I have also attached the
> output of "$relax -i". Kindly suggest something to resolve this problem.

Hi Aritra,

Did you work out how to correctly install wxPython in the end?  I have
never seen this std::bad_alloc when using different wxPython versions
for almost a decade, so I cannot really help you debug your private
wxPython software installation.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 10:16, Edward d'Auvergne  wrote:
> On 29 September 2016 at 09:55, Gary Thompson  wrote:
>> Hi Sam
>>
>> have you tried with only one set of coordinates (i presume these are both 
>> homo dimers with some form of symetry plane or axis?
>
> Looking at the file attached to https://gna.org/bugs/?25133, the
> problem is at the start of the script:
>
> """
> relax> structure.read_pdb(file='cluster1_12.pdb', dir=None,
> read_mol=None, set_mol_name='hRGS4', read_model=None,
> set_model_num=None, alt_loc=None, verbosity=1, merge=False)
>
> Internal relax PDB parser.
> Opening the file 'cluster1_12.pdb' for reading.
> Adding molecule 'hRGS4' (from the original molecule number 1).
> Merging with molecule 'hRGS4' (from the original molecule number 2).
> """
>
> Note the text "Merging".  This is because you are setting all
> molecules in the PDB file to the single molecule name "hRGS4".  What
> you need to do is read a single molecule (via the 'read_mol'
> argument).  Note Gary's text about symmetry.  If you have a homo dimer
> without symmetry, there is absolutely no theory on the planet
> currently developed to handle relaxation data in this situation.

Running the RGS4_modelfree_sample_script.py script with the
"read_mol=1" argument for the structure.read_pdb user function causes
the IndexError to go away.  Unfortunately I don't have the time to
investigate and turn this into a self-explanatory check and RelaxError
yet.

Cheers,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 29 September 2016 at 09:55, Gary Thompson  wrote:
> Hi Sam
>
> have you tried with only one set of coordinates (i presume these are both 
> homo dimers with some form of symetry plane or axis?

Looking at the file attached to https://gna.org/bugs/?25133, the
problem is at the start of the script:

"""
relax> structure.read_pdb(file='cluster1_12.pdb', dir=None,
read_mol=None, set_mol_name='hRGS4', read_model=None,
set_model_num=None, alt_loc=None, verbosity=1, merge=False)

Internal relax PDB parser.
Opening the file 'cluster1_12.pdb' for reading.
Adding molecule 'hRGS4' (from the original molecule number 1).
Merging with molecule 'hRGS4' (from the original molecule number 2).
"""

Note the text "Merging".  This is because you are setting all
molecules in the PDB file to the single molecule name "hRGS4".  What
you need to do is read a single molecule (via the 'read_mol'
argument).  Note Gary's text about symmetry.  If you have a homo dimer
without symmetry, there is absolutely no theory on the planet
currently developed to handle relaxation data in this situation.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 29 September 2016 at 00:23, Mahdi, Sam  wrote:
> Hi Troels,
> Update on both proteins: So for protein 1, I can upload all the spins (H
> and N), but then I recieve an error. This is the error I recieved for
> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
> (set A) and set (B) (e.g.
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
> protein has 4 sets, A,B,C, and D ours only have A and B). For both these
> proteins I recieve this error
>  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
> self.callback.init_master(self)
>   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> default_init_master
> self.master.run()
>   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
> self.interpreter.run(self.script_file)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in run
> return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> run_script
> return console.interact(intro, local, script_file,
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> interact_script
> exec_script(script_file, local)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> exec_script
> runpy.run_module(module, globals)
>   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
> fname, loader, pkg_name)
>   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
>   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> 31, in 
>
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 246, in __init__
> self.execute()
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 600, in execute
> self.multi_model(local_tm=True)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 888, in multi_model
> self.interpreter.minimise.grid_search(inc=self.grid_inc)
>   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> __call__
> self._backend(*new_args, **uf_kargs)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172, in
> grid_search
> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> verbosity=verbosity, skip_preset=skip_preset)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, in
> grid_setup
> elif values[i] in [None, {}, []]:
> IndexError: index out of bounds
>
> Which from my understanding basically means, the co-ordinates of the spins
> are out of the acceptable range for relax. I've checked all the
> co-ordinates for both, nothing is extreme or outlandish (all within a range
> of -20 to 20).
> Is relax unable to process pdb files that are dimers (with 2 sets A and
> B).? Furthermore, is it unable to process trimers and tetramers?

Hi,

For the model-free analysis in relax, as well as all other analyses,
we have designed the program to try to catch all user input errors and
to produce a specific RelaxError prior to minimisation explaining
exactly what went wrong.  An IndexError here simply shows that not all
erroneous data input has been caught.  Let me go back to your PDB
file.  You should not edit this file unless you know exactly what you
are doing, but relax will handle all PDB files.  There is no need to
rename protons.  You just specify the correct proton name in the input
script.  I may have missed it as there is a lot of correspondence I
have to catch up on, but did you upload your script and a truncated
set of data to the relax bug or support trackers?  Do you have a
mini-data set (1 or 2 residues) and script that triggers this error?
If we can reproduce the IndexError, then finding the error would be
easy.

Cheers,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 01:35, Mahdi, Sam  wrote:
> Also, Congrats to Edward!

Thanks :)

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 22:44, Mahdi, Sam  wrote:
> Hey Troels,
>
> I ran the relax -x and recieve this error at the GUI tests
> =
> = GUI tests =
> =
>
> **
> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
> failed: (r == n_visible_rows)
> Abort (core dumped)
> crowlab: [~/relax-4.0.2]>

That is a strange error, but it shouldn't effect you.  It is a minor
problem with your wxPython setup and GTK+ on your system.  It's only
an issue if you are running the GUI and the GUI suddenly crashes on
you.  But again, this problem is not due to relax.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 20:32, Troels Emtekær Linnet
 wrote:
> If you get different results, for the same setup, this is not good.
> Not at all !

Hi,

Sorry for not being more involved, I've been in what could be called
paternity leave.  This point is very, very important.  With the same
setup you must absolutely always obtain the same result.  There are
numerical precision differences between operating systems, CPU types,
and Python 2 vs. 3, but this should be very small.

Regards,

Edward

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Re: Using multi-processor for nmr relax

[Edward d'Auvergne]

On 30 August 2016 at 17:08, Mahdi, Sam  wrote:
> Hi Edward,
>
> Thanks for the quick reply. In the "Further Details" section that shows the
> email archive. When Dr. Thompson is setting up the code to run relax in a
> multi-processor mode he uses the commands "lamboot" and "lamhalt". From what
> I could find, these are commands from the lam/mpi program and not open mpi.
> I know in the manual in "usage of the multi-processor" page, it shows the
> open mpi command "mpirun", but that is the only indication I've seen of
> using open mpi to start relax in multi-processor mode.

I think the old mpi4py can handle these older MPI implementations as
well.  Anyway, you only need that "mpirun" command.

Regards,

Edward

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Re: Using multi-processor for nmr relax

[Edward d'Auvergne]

On 30 August 2016 at 02:57, Mahdi, Sam  wrote:
> Hello everyone,
>
> I was looking to attempt to run relax on a multi-processor platform. I was
> looking at Gary Thompsons overview, and I realized it uses lam/mpi format
> which is no longer provided. I've decided to use it's replacement, open
> mpi. Is there any updated overview that uses open mpi? One that shows a
> step by step guide for how to setup relax to run on multi-processors (with
> commands and outputs showed).

Hi Sam,

Gary Thompson's multi-processor system is based on OpenMPI.  Please see:

http://www.nmr-relax.com/manual/The_multi_processor_framework.html

Which instructions are you referring to?

Regards,

Edward



>
> Thank you
> Sam
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Re: Troubleshooting model-free analysis

[Edward d'Auvergne]

On 8 August 2016 at 21:04, Mahdi, Sam  wrote:
> Hi, I had some general questions regarding model-free analysis that came up
> as I was running it. About 2 months ago, I ran model-free on a 126 residue
> protein. The pdb file I used for the protein had an extra 7 residue
> modifier at one of the terminals, which made it 133 residues; thus, my data
> did not match the pdf file. That run took a little over a week, with the
> sphere model running about 2 models, along with every other model being
> about 2. The data for this run I obtained was unusable (values as small as
> 5x10^-30 for S^2). I attributed this to the fact that my pdf files sequence
> did not align with my data.

Do you mean that the residue numbers were out by 7?  I have considered
this, but relax currently has no way of renumbering the residues in a
3D structure or renumbering the residues of the input data.  So
unfortunately you'll either have to use a molecular view to change
your PDF file, or a script or spreadsheet to renumber your input data.


> I adjusted my relax data (simply added 7 residues with no values), and ran
> it again (all settings the same as before, everything automatic).

I don't think that your data will match up to the correct residues.
The residue numbers in the PDB file and the input relaxation data must
be exact matches.

> This time
> it has taken almost a month, with the sphere model on its 20th run. I saw
> in a previous email that the max is 30 iterations. Is it normal to hit the
> max? Does this mean my data is bad if it requires the max 30 iterations?
> Also, why is it running up to 20 now? The 7 residues I added didn't have
> data, so it doesn't run models for them. I assumed there would be a
> difference in time since the data is now attributed to different spins, but
> not this much of a difference.

If the 3D info and input data do not match, then the results for
non-isotropic (ellipsoidal and spheroidal diffusion) will make no
sense.  In relax you should never need to add relaxation data for
these 7 residues, as relax will handle this situation automatically.
What does your input relaxation data look like?

Regards,

Edward

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Re: error in final execution of NOE in relax

[Edward d'Auvergne]

On 24 June 2016 at 06:49, Rakesh Sharma  wrote:
> Dear all,
>
> I am getting an error in final step of NOE which is the "execution" step.
> the error reads as follows:
>
> Traceback (most recent call last):
>   File "gui/analyses/execute.py", line 87, in run
> self.run_analysis()
>   File "gui/analyses/auto_noe.py", line 378, in run_analysis
> NOE_calc(pipe_name=self.data.pipe_name,
> pipe_bundle=self.data.pipe_bundle, file_root=self.data.file_root,
> results_dir=self.data.save_dir, save_state=False)
>   File "auto_analyses/noe.py", line 90, in __init__
> self.run()
>   File "auto_analyses/noe.py", line 105, in run
> self.interpreter.minimise.calculate()
>   File "prompt/uf_objects.py", line 225, in __call__
> self._backend(*new_args, **uf_kargs)
>   File "pipe_control/minimise.py", line 102, in calc
> api = return_api()
>   File "specific_analyses/api.py", line 133, in return_api
> from specific_analyses.noe.api import Noe
> ImportError: No module named api
>
>
> I have loaded my ref and sat files and when i  try to execute i am getting
> this error every time.
> basic informations:
> I have used all files from test suite itself.
> and the loaded spins are from a structure file 172 spin system
> every step same as mentioned in program noe.py  or manual gui.
>
> if anyone can help me please reply .
> waiting for your reply.

Hi Rakesh (or Akshay?),

Sorry for the late reply, I have been quite busy over the last two
months and have been unable to reply to any messages.  For this error,
which version of relax are you using?  And which operating system are
you running on?  What do you see when you run:

$ relax -i --tee log

This error is quite strange, as the file that cannot be imported
should exist on the system:

[edward@localhost relax-trunk]$ ls specific_analyses/noe/api.py
specific_analyses/noe/api.py

Can you run the test suite?  The following should give zero errors:

$ relax --test-suite --tee tests.log

From the error itself, this simply means that the file
specific_analyses/noe/api.py is missing.  Are you sure your downloaded
relax distribution file is not corrupt?  Does the md5sum value match
the published value:

http://www.nmr-relax.com/download.html

Regards,

Edward

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Re: Troubleshooting model-free analysis

[Edward d'Auvergne]

Hi Sam,

Welcome to the relax mailing lists.  Sorry for the late reply, I've
been quite busy for the last two months.  Please see below:

On 2 July 2016 at 02:41, Mahdi, Sam  wrote:
> I had 2 questions regarding the relax model-free analysis.
> 1: When uploading a pdb file for the spin system, is there a certain way to
> have some residues spins ignored?

I guess you mean reading the spin system from a PDB file.  You can do
this when running the structure.load_spins user function via the
spin_id parameter:

http://www.nmr-relax.com/manual/structure_load_spins.html

Or you can do this afterwards, either using the deselect.spin or
spin.delete user functions:

http://www.nmr-relax.com/manual/deselect_spin.html
http://www.nmr-relax.com/manual/spin_delete.html

> i.e. give it a certain range. E.g. The
> structural data for the pdb file I want uses an extra linker at the
> C-terminus of my protein that is about 7 residues long. The relaxation data
> I have however is for the protein without those 7 extra residues (thus
> residue 7 for the pdb file is residue 1 for my relaxation data). Is there a
> way I can get the relax program to ignore the first 7 residues?

If this is a model-free analysis, the residues without data will be
automatically deselected prior to optimisation (you'll see this in the
logs).

> I tried
> typing in the range I wanted (residue 8 to residue 133 inputed as [8-133])
> in the molecule number to read option, but when I did that, it gave me this
> error RelaxError: No PDB file has been loaded. When I removed the range, it
> uploaded the file but with all the residues, including the linker I didn't
> want.

Ah, I think you might be confusing the loading of a structural file
and the creation of NMR-active spin systems.   All atoms of the
structural file will be loaded into relax, but none of these atoms
will be set a spin systems.  You then have to use the
structure.load_spins user function to pick our the NH atoms pairs of
interest.


> 2: The relaxation data I have is for the backbone (NH), thus the values I
> have for the backbone are for that bond. The pdb file I uploaded has both
> of their spins. The relaxation data I have is one value for each residue
> (for the NH bond). So I assumed that value is the same for both the
> Nitrogen and Hydrogen spin of that residue. E.g. If residue 3 has a R1
> value of 1.03, I assume the nitrogen spin and hydrogen spin both have an R1
> value of 1.03.

This is not correct.  The proton relaxation values will be very
different.  Note that almost no one collects this data as the proton
spin cannot be considered as isolated.  Therefore the normal
assumptions for a model-free analysis of an isolated two spin system
do no hold.  E.g. spin diffusion is an important effect in protons.
This is also why carbon relaxation and model-free analyses are only
performed at natural abundance, to ensure that the system is isolated.

> When I upload the relaxation data with the Nitrogen @N spin
> id string it works fine, each residue has the proper value. However, the
> value for the hydrogen is 0 for each residue.  I tried to create a new data
> set, this time with the spin id string for Hydrogen using the same R1 file
> I had used for the nitrogen, but when I did this I was given this error:
> RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
> invalid, the residue number data 'Residue' is invalid.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> Traceback (most recent call last):
>   File "/usr/local/Relax/relax-2.2.5/gui/wizard.py", line 163, in _apply
> self.exec_status = self.on_execute()
>   File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 867, in
> on_execute
> return_status = self.execute(self.name, **kargs)
>   File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 797, in
> execute
> return_status = interpreter.apply(uf, *args, **kwds)
>   File "/usr/local/Relax/relax-2.2.5/gui/interpreter.py", line 112, in apply
> apply(fn, args, kwds)
>   File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 1033,
> in read
> pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
> res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
> spin_names=spin_names, spin_id=spin_id)
>   File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 870,
> in pack_data
> new_id = new_ids[0]
> IndexError: list index out of range

You should simply not load any data for the proton.  Then the analysis
will deselect those H spins prior to o

Re: Issue in ModelFree Calculation

[Edward d'Auvergne]

On 20 July 2016 at 16:02, Troels Emtekær Linnet  wrote:
> Hi.
>
> Did you compile relax yourself?
> Try compiled version of relax.
>
> Have you tried running the systemtests?
> http://wiki.nmr-relax.com/Installation_test
>
> It looks like you are running mpirun.
> Try running without.
>
> Or look here:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing
>
> http://wiki.nmr-relax.com/OpenMPI#Relax_In_multiprocessor_mode
>
> 2016-07-20 15:18 GMT+02:00 :
>
>> Dear all,I am a new user of Relax and I am trying to perform ModelFree
>> calculation with a 207 residue protein using both fully automated and
>> manual protocol of Relax GUI mode. But every time the calculation is
>> stopped with a "bad_alloc" error. The details of the is as follows:
>> terminate called after throwing an instance of 'std::bad_alloc'what():
>>  std::bad_alloc*** Process received signal ***Signal: Aborted (6)Signal
>> code:
>>  
>> (-6)[0x2e040c]/lib/libc.so.6(abort+0x17a)[0xb415ea]/usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x167)[0x65c0397]/usr/lib/libstdc++.so.6(+0x57f226)[0x65be226]/usr/lib/libstdc++.so.6(+0x57f263)[0x65be263]/usr/lib/libstdc++.so.6(+0x57f3a2)[0x65be3a2]/usr/lib/libstdc++.so.6(_Znwj+0x87)[0x65be937]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE4_Rep9_S_createEjjRKS1_+0x79)[0x65b35a9]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE9_M_mutateEjjj+0x51)[0x65b5471]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE15_M_replace_safeEjjPKwj+0x3b)[0x65b562b]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE6assignEPKwj+0x5f)[0x65b56ef]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x3a535)[0x1fc8535]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x40714)[0x1fce714]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x7c1bd)[0x200a1bd]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x7c38f)[0x200a38f]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x83a3f)[0x2011a3f]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x98d24)[0x2026d24]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x3f03e)[0x1fcd03e]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(_ZNK16wxStyledTextCtrl7SendMsgEiml+0x2f)[0x1fae5ff]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(_ZN16wxStyledTextCtrl17SetSelectionStartEi+0x34)[0x1fb0f34]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x33dd4)[0x1fc1dd4]/usr/lib/python2.6/site-packages/wx-3.0-gtk2/wx/_core_.so(+0x10a489)[0x10b0489]/usr/lib/libpython2.6.so.1.0(PyCFunction_Call+0x148)[0x2d77218]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x499f)[0x2dd475f]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x48de)[0x2dd469e]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x48de)[0x2dd469e]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0[0x2d63397]***
>> End of error message
>> ***--mpirun
>> noticed that process rank 0 with PID 15605 on node madhava exited on signal
>> 6
>> (Aborted).--
>> So kindly suggest some details about the error and suggest specific hints
>> to resolve the problem.Thanks in advance.
>> Aritra BejDoctoral FellowCSIR - IICB

Hi Aritra,

Did you get a change to look at Troels' suggestions?  Do you see this
error when you run the test suite?  To me this looks like a faulty
installation of wxPython.  These errors and the files listed have
nothing to do with relax.  What is your output when you run:

$ relax -i

Can you run the wxPython demo or the wxPython tests to make sure this
is set up correctly?

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 6 June 2016 at 12:37, Petr Padrta  wrote:
> On Fri, Jun 03, 2016 at 04:43:18PM +0200, Edward d'Auvergne wrote:
>> On 3 June 2016 at 12:08, Edward d'Auvergne  wrote:
>> > Hi Petr,
>> >
>> > For the new bug report at https://gna.org/bugs/?24675, now looking at
>> > the results I can see that this is actually quite a deliberate
>> > feature.  For reference, I will attach the plots for residues 133 and
>> > 134 for the CR2 model as a PDF file to that bug report
>> > (disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf).  For residue 133,
>> > there the blue line can be seen to be the dispersion curve predicted
>> > for the missing 600 MHz data.  For 134, the green line is the
>> > predicted dispersion curve for the 950 MHz data.
>> >
>> > The R20 values come from the fitting of the single field strength data
>> > points, and this value is independent of field strength.  So the
>> > predicted curves are perfectly correct - they are exactly where they
>> > are supposed to be.  Assuming the model to be correct, the predicted
>> > curves are what the real data should look like.  So the curves without
>> > measured data are actually quite powerful tools for investigating why
>> > the data is missing.  They are also useful for investigating how well
>> > the model fits to single field strength data.  It is also quite easy
>> > in Grace to double click on the curve and hide it, if desired.
>> > Therefore I think I'll leave the plotting code as it is.
>>
>> Hi Petr,
>>
>> Sorry, the R20 values are field strength dependent, but both are fit
>> during the optimisation of the dispersion models with missing data.
>> This is problematic as one parameter is undefined - the R20 for the
>> missing field - and this interferes with optimisation algorithms.  The
>> undefined R20 value can float around to any value, and this breaks the
>> rules that most algorithms absolutely rely on.  Hence the solution
>> found is unlikely to be the minimum in the optimisation space.  I
>> would therefore suggest deselecting these spins for now, as the
>> results are nonsensical.  It might take me a while to update each part
>> of relax to detect the missing data for one entire field strength from
>> the N fields, and drop back to N-1 fields.  This bug might take a
>> while to fix!  I might have to spend a few days working on that one
>> next week.
>>
>> Regards,
>>
>> Edward
>
> Hello Edward,
>
> Hey, that would be nice if R20 were really independent of B0 ;-)
>
> Well, the undefined R20 can float to any value but within the bounds (0-200) 
> so
> at least some algorithms should be able to tackle that, Nelder-Mead very
> probably amongst them. This seems to be corroborated also by real data. I.e.
> when analysing our complete data, (so far) I'm getting sensible results,
> comparable to calculating separate residues, of course not counting the R20s
> for missing B0s, which sometimes float to 0, at other times go to 200. That's
> why I suggested in my bugreports and mails that for the case of leaving all
> R20s in, it is probably better to force them to 0. Of course it's even better
> to remove missing R20s completely but I expected that to be much more effort.

Hi,

The Nelder-Mead simplex tends to have severe problems along these
undefined regions (which in this model is across the entire
optimisation space).  The simplex algorithm can get quite confused.
If the global minimum is found, then that is pure luck, as reasonable
convergence properties of this algorithm are only guaranteed in a
continuous and smooth space.  What relax should do is dynamically fall
back to N-1 fields for spin systems missing a single whole field of
data.  But currently the number of fields is defined at the global
whole-system level.  Most of relax can already currently handle this
dynamic algorithm, it is just the packing and unpacking of data for
optimisation that would need to be rewritten.  Until that is done, I
would suggest avoiding those data points, or perform a separate single
field strength analysis on them.  You may find the same result, but I
would not trust relax for these data points yet.

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 3 June 2016 at 12:08, Edward d'Auvergne  wrote:
> Hi Petr,
>
> For the new bug report at https://gna.org/bugs/?24675, now looking at
> the results I can see that this is actually quite a deliberate
> feature.  For reference, I will attach the plots for residues 133 and
> 134 for the CR2 model as a PDF file to that bug report
> (disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf).  For residue 133,
> there the blue line can be seen to be the dispersion curve predicted
> for the missing 600 MHz data.  For 134, the green line is the
> predicted dispersion curve for the 950 MHz data.
>
> The R20 values come from the fitting of the single field strength data
> points, and this value is independent of field strength.  So the
> predicted curves are perfectly correct - they are exactly where they
> are supposed to be.  Assuming the model to be correct, the predicted
> curves are what the real data should look like.  So the curves without
> measured data are actually quite powerful tools for investigating why
> the data is missing.  They are also useful for investigating how well
> the model fits to single field strength data.  It is also quite easy
> in Grace to double click on the curve and hide it, if desired.
> Therefore I think I'll leave the plotting code as it is.

Hi Petr,

Sorry, the R20 values are field strength dependent, but both are fit
during the optimisation of the dispersion models with missing data.
This is problematic as one parameter is undefined - the R20 for the
missing field - and this interferes with optimisation algorithms.  The
undefined R20 value can float around to any value, and this breaks the
rules that most algorithms absolutely rely on.  Hence the solution
found is unlikely to be the minimum in the optimisation space.  I
would therefore suggest deselecting these spins for now, as the
results are nonsensical.  It might take me a while to update each part
of relax to detect the missing data for one entire field strength from
the N fields, and drop back to N-1 fields.  This bug might take a
while to fix!  I might have to spend a few days working on that one
next week.

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

Hi Petr,

For the new bug report at https://gna.org/bugs/?24675, now looking at
the results I can see that this is actually quite a deliberate
feature.  For reference, I will attach the plots for residues 133 and
134 for the CR2 model as a PDF file to that bug report
(disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf).  For residue 133,
there the blue line can be seen to be the dispersion curve predicted
for the missing 600 MHz data.  For 134, the green line is the
predicted dispersion curve for the 950 MHz data.

The R20 values come from the fitting of the single field strength data
points, and this value is independent of field strength.  So the
predicted curves are perfectly correct - they are exactly where they
are supposed to be.  Assuming the model to be correct, the predicted
curves are what the real data should look like.  So the curves without
measured data are actually quite powerful tools for investigating why
the data is missing.  They are also useful for investigating how well
the model fits to single field strength data.  It is also quite easy
in Grace to double click on the curve and hide it, if desired.
Therefore I think I'll leave the plotting code as it is.

Cheers,

Edward



On 2 May 2016 at 17:37, Edward d'Auvergne  wrote:
> On 29 April 2016 at 11:58, Petr Padrta  wrote:
>> On Wed, Apr 27, 2016 at 11:27:09AM +0200, Edward d'Auvergne wrote:
>>> On 22 April 2016 at 20:43, Petr Padrta  wrote:
>>> > Hi Edward,
>>> >
>>> > OK,  I finally managed to create a bug report on gna with attached 
>>> > example.
>>>
>>> Hi Petr,
>>>
>>> Thank you for that.  For reference, the report is at
>>> https://gna.org/bugs/?24601 .  I have taken your data and script and
>>> created the following relax system test:
>>>
>>> $ relax -s Relax_disp.test_bug_24601_r2eff_missing_data
>>>
>>> I used this to catch the bug you saw and to fix all the issues.  Note
>>> that it took a bit longer than normal as the first error you saw was
>>> only one of 3.  I also had to update the Monte Carlo simulation error
>>> analysis code, and the Grace plotting code.  I have committed the
>>> changes:
>>>
>>> http://article.gmane.org/gmane.science.nmr.relax.scm/25955
>>>
>>> When using this, please carefully check that all is working as
>>> expected.  The system test now passes, however there might be other
>>> strangeness (for example, check your Grace graphs for incorrect data
>>> labels).  For any other issues you see, if you could create a separate
>>> bug report for each, that would be appreciated.  As before, if you
>>> could include truncated data and a script to replicate the issue, that
>>> would be much appreciated as I could then create the system test to
>>> help fix the problem.  The more bugs reported - from critical to
>>> superficial - the smoother we can make the analysis process!  Even
>>> confusing text messages by relax deserve a report.
>>>
>>> For obtaining the code, if you need this soon, I would suggest
>>> directly obtaining it from the source code repository:
>>>
>>> http://www.nmr-relax.com/download.html#Source_code_repository
>>>
>>> The reason is because there are a few newly introduced bugs that I
>>> would like solved before we release relax 4.0.2.  So it might take a
>>> few weeks before the new release is out.
>>>
>>> Regards,
>>>
>>> Edward
>>
>> Hi Edward,
>>
>> Thanks! I fetched last SVN version (r28204) and so far it seems that your new
>> dispersion code works as expected. The (rhetorical) question is what to do 
>> with
>> interpolated dispersion curves from missing B0 fields - they have the right
>> shape but are shifted along R2eff-axis as their r20 is unknown. Hmm, I can
>> always delete them from the grace plots. Or maybe I'll do another bug report
>> after some more testing.
>
> Hi Petr,
>
> A new bug report for such things would be much appreciated.  I can
> then list the bugs one after the other and their details in the
> release notes.  It also makes it incredibly easy for a developer to
> fix the bug if truncated, minimal data sets and a script and/or
> instructions are attached to the bug report.  That way a system test
> can be quickly constructed to reproducibly capture the bug.  In most
> cases where a system test can be set up, the fix then only requires
> 5-10 minutes to resolve.
>
> Cheers,
>
> Edward

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Re: Data files

[Edward d'Auvergne]

Hi Rakesh,

As Troels mentioned, the test suite directories contain a huge number
of examples.  A good one is the OMP data from Gitti et al. (2005), in
test_suite/shared_data/model_free/OMP (see my PhD thesis at
https://minerva-access.unimelb.edu.au/handle/11343/39174 ).
Alternatively, you could download data from the BMRB.  You can then
follow the tutorials for model-free analyses from the relax manual:

The new protocol in the prompt/script UI mode - (
http://www.nmr-relax.com/manual/The_new_protocol_in_the_prompt_script_UI_mode.html
)
The new protocol in the GUI - (
http://www.nmr-relax.com/manual/The_new_protocol_in_the_GUI.html )

You will have to play around with the starting steps, as setting up
spin systems can take two major routes - from a PDB file (with atomic
coordinates), or from a text file containing your primary sequence (no
positional information, but loading the positions from a PDB file
later).  I hope this helps.

Regards,

Edward



On 29 May 2016 at 21:12, Troels Emtekær Linnet  wrote:
> Hi Rakes.
>
> Look in the test_suite folder.
>
> Hundreds of unit and system test is provided there.
>
> Best
> Troels
>
> 2016-05-27 14:21 GMT+02:00 Rakesh Sharma :
>
>> Hi everyone,
>> can anybody have idea that from where to get data files used in relax
>> manual calculations. I am new to relax and learning it. I get structure
>> file from protein data bank for molecule used in relax and learned up to
>> spin loading. Now for further analysis i need sparky list files for T1, T2
>> and Noe. Does anybody has idea that from where i can get these and  process
>> with same as in manual.
>> Regards,
>> Rakesh Sharma
>>
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> Virus-free.
>> www.avast.com
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 29 April 2016 at 11:58, Petr Padrta  wrote:
> On Wed, Apr 27, 2016 at 11:27:09AM +0200, Edward d'Auvergne wrote:
>> On 22 April 2016 at 20:43, Petr Padrta  wrote:
>> > Hi Edward,
>> >
>> > OK,  I finally managed to create a bug report on gna with attached example.
>>
>> Hi Petr,
>>
>> Thank you for that.  For reference, the report is at
>> https://gna.org/bugs/?24601 .  I have taken your data and script and
>> created the following relax system test:
>>
>> $ relax -s Relax_disp.test_bug_24601_r2eff_missing_data
>>
>> I used this to catch the bug you saw and to fix all the issues.  Note
>> that it took a bit longer than normal as the first error you saw was
>> only one of 3.  I also had to update the Monte Carlo simulation error
>> analysis code, and the Grace plotting code.  I have committed the
>> changes:
>>
>> http://article.gmane.org/gmane.science.nmr.relax.scm/25955
>>
>> When using this, please carefully check that all is working as
>> expected.  The system test now passes, however there might be other
>> strangeness (for example, check your Grace graphs for incorrect data
>> labels).  For any other issues you see, if you could create a separate
>> bug report for each, that would be appreciated.  As before, if you
>> could include truncated data and a script to replicate the issue, that
>> would be much appreciated as I could then create the system test to
>> help fix the problem.  The more bugs reported - from critical to
>> superficial - the smoother we can make the analysis process!  Even
>> confusing text messages by relax deserve a report.
>>
>> For obtaining the code, if you need this soon, I would suggest
>> directly obtaining it from the source code repository:
>>
>> http://www.nmr-relax.com/download.html#Source_code_repository
>>
>> The reason is because there are a few newly introduced bugs that I
>> would like solved before we release relax 4.0.2.  So it might take a
>> few weeks before the new release is out.
>>
>> Regards,
>>
>> Edward
>
> Hi Edward,
>
> Thanks! I fetched last SVN version (r28204) and so far it seems that your new
> dispersion code works as expected. The (rhetorical) question is what to do 
> with
> interpolated dispersion curves from missing B0 fields - they have the right
> shape but are shifted along R2eff-axis as their r20 is unknown. Hmm, I can
> always delete them from the grace plots. Or maybe I'll do another bug report
> after some more testing.

Hi Petr,

A new bug report for such things would be much appreciated.  I can
then list the bugs one after the other and their details in the
release notes.  It also makes it incredibly easy for a developer to
fix the bug if truncated, minimal data sets and a script and/or
instructions are attached to the bug report.  That way a system test
can be quickly constructed to reproducibly capture the bug.  In most
cases where a system test can be set up, the fix then only requires
5-10 minutes to resolve.

Cheers,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 22 April 2016 at 20:43, Petr Padrta  wrote:
> Hi Edward,
>
> OK,  I finally managed to create a bug report on gna with attached example.

Hi Petr,

Thank you for that.  For reference, the report is at
https://gna.org/bugs/?24601 .  I have taken your data and script and
created the following relax system test:

$ relax -s Relax_disp.test_bug_24601_r2eff_missing_data

I used this to catch the bug you saw and to fix all the issues.  Note
that it took a bit longer than normal as the first error you saw was
only one of 3.  I also had to update the Monte Carlo simulation error
analysis code, and the Grace plotting code.  I have committed the
changes:

http://article.gmane.org/gmane.science.nmr.relax.scm/25955

When using this, please carefully check that all is working as
expected.  The system test now passes, however there might be other
strangeness (for example, check your Grace graphs for incorrect data
labels).  For any other issues you see, if you could create a separate
bug report for each, that would be appreciated.  As before, if you
could include truncated data and a script to replicate the issue, that
would be much appreciated as I could then create the system test to
help fix the problem.  The more bugs reported - from critical to
superficial - the smoother we can make the analysis process!  Even
confusing text messages by relax deserve a report.

For obtaining the code, if you need this soon, I would suggest
directly obtaining it from the source code repository:

http://www.nmr-relax.com/download.html#Source_code_repository

The reason is because there are a few newly introduced bugs that I
would like solved before we release relax 4.0.2.  So it might take a
few weeks before the new release is out.

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

Hi Petr,

Welcome to the relax mailing lists!  For your problem, what does relax
say if you run the analysis with missing residues?  Could you copy and
paste the full output?  Cheers.  We have written the software to
specifically handle this situation, and this should be automatic.  For
the relax developers reading this, for reference you can see this as
the "missing" argument for the target function __init__() setup method
at:


http://www.nmr-relax.com/api/4.0/target_functions.relax_disp-pysrc.html#Dispersion.__init__

If you see an error message, then this is a bug.  relax is designed to
handle every situation automatically - you should never, ever have to
revert to such tricks to get relax to work.  If you do see an error,
it would be appreciated if you could create a bug report about the
problem at:

https://gna.org/bugs/?func=additem&group=relax

Ideally, if you could attach a script and truncated data files (with
maximally 2-3 residues, slightly randomised, if you wish), that would
be appreciated.  If the problem can be quickly reproduced with the
attached files, then I can convert that in to a relax system test.  I
normally then only need 5-10 minutes to eliminate such a bug.

Cheers,

Edward






On 22 April 2016 at 14:18, Petr Padrta  wrote:
> Hello everybody,
>
> I'm analysing some CPMG data with the auto-analysis script
> (sample_scripts/relax_disp/cpmg_analysis.py). Problem is that I don't have the
> same set of spectra for all my residues, i.e. there are missing residues in
> some of the peak lists and relax doesn't like that. So far I bypass the 
> problem
> by generating residue-specific peak lists and running the analyses separately
> for individual residues but that's 1) tedious and 2) I'm unable to run
> clustered analysis unless I shave the spectra list to "common denominator". I
> also tried setting the missing intensities to "None" or to "NA" but that's not
> working. Any ideas?
>
> --
>
>  Petr Padrta
>
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Re: Fixing phi_ex or k_ex on R1rho fits

[Edward d'Auvergne]

On 20 April 2016 at 14:42, Troels Emtekær Linnet  wrote:
> Hi Vilius.
>
> You can restrict the phi_ex/k_ex with value.set before grid search.
> It will though be set free again in minimisation.

True, we have this feature set up for the relaxation dispersion
analysis to allow parameters to be fixed to the input value during
optimisation (it is solely for the dispersion analysis).  I'd
forgotten about that.  For restricting the value to a range of
numbers, the constraints code can be modified.  In any case,
off-resonance, multi-field data should improve the analysis of R1rho
data.  Fixing a parameter in such a situation might simply hide an
important problem with the input data.

Regards,

Edward

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Re: regarding installation

[Edward d'Auvergne]

On 20 April 2016 at 12:39, Rakesh Sharma  wrote:
>
> Thanks for your reply. I am not able to run relax so not able to generate log 
> file. I Downloaded relax then put that in system path by using my computer as 
> told in manual. I have python 2.7.11 Numpy 1.11.0, Relax is 4.0.1. Can you 
> please tell me the procedure after installing python how to install that in 
> window. I can download other version of python and all software. When I 
> started installing, I got problem with cythonize then when I rectify that 
> then with numpy now it is showing some error with code at line 59 and 72 in 
> dep-chk.py when i am typing relax in cmd. Please tell me step wise 
> installation procedure so that I can check I followed the right path or not.

Hi,

Are you using the official Python from http://python.org ?  If not,
then that is very likely to be your problem.  Can you run Python, and
type "import numpy"?  Does this show any error messages?

Regards,

Edward

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Re: Spectral data corresponding to the ID string xxx does not exist

[Edward d'Auvergne]

Hi,

Thank you Troels for looking after this.  As I didn't see any of
Karin's follow up emails, I assume that everything is now ok.  Karin,
if there are still problems, please consider creating a bug report at:

https://gna.org/bugs/?func=additem&group=relax

There you'll be able to attach your files, scripts, etc.  Note that
this will make any of your data public, so it is often a good idea to
truncate the files to 1 or 2 spin systems, and make sure that the
truncated file still trigger the problem you see.

Regards,

Edward



On 1 April 2016 at 01:45, Troels Emtekær Linnet  wrote:
> Dear Karin.
>
> Thank you for your last feedback.
>
> You are absolutely right.
> relax can indeed read NMRView type of files.
>
> My last comment on this was an error.
>
> I have produced a Tutorial page for you on the wiki:
> http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_from_NMRView_files
>
> Under the point: Run analysis in relax GUI
> You can expand "the script" code by clicking "show" in the right side.
>
> These small snippets of codes is there to help reading "many" files.
> This is tedious work, when this is done manually.
>
> As I don't have all the files, I cannot test any further from this.
>
> Let me know how it goes. :)
>
> Best
> Troels
>
>
> 2016-03-31 22:35 GMT+02:00 Troels Emtekær Linnet :
>
>> Hi Karin.
>>
>> Thank you for the file.
>>
>> The problem is, that relax currently does not recognize the file type of
>> NMRView.
>>
>> But the files contains all the information we need.
>>
>> We then have 2 options.
>>
>> 1) Either to make some custom scripts, that can convert the files to a
>> format that relax understands
>> 2) Or develop relax to understand NMRView files.
>>
>> My problem is, that I cannot find any documentation of the file type.
>> Can you help me with this?
>>
>> I am starting to writing down notes, so I can make a tutorial.
>>
>> 
>>
>> This message can be found at:
>> http://thread.gmane.org/gmane.science.nmr.relax.user/1874
>>
>> Similar Tutorials for R1 can be found here:
>> http://wiki.nmr-relax.com/Main_Page
>> http://wiki.nmr-relax.com/Category:Tutorials
>>
>> http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_on_varian_recorded_as_fid_interleaved
>>
>> This does not cover the current problem.
>> Relax cannot read NMRView *.xpk files.
>>
>> A similar problem can be seen here:
>>
>> http://wiki.nmr-relax.com/Tutorial_for_sorting_data_stored_as_numpy_to_on-resonance_R1rho_analysis
>>
>> We need to make modifications.
>> The whole list of files is:
>>
>> R1-methyl_hRGS4_20C_pH7_Mar2016_0ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_10msa
>> R1-methyl_hRGS4_20C_pH7_Mar2016_10msb
>> R1-methyl_hRGS4_20C_pH7_Mar2016_30ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_50ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_70ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_90msa
>> R1-methyl_hRGS4_20C_pH7_Mar2016_90msb
>> R1-methyl_hRGS4_20C_pH7_Mar2016_110ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_130ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_150ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_170ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_190ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_210ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_250ms
>>
>> Each file has a structure like this:
>>
>> 
>> label dataset sw sf
>> H1 C13
>> R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.nv
>> 1500.2322998 3328.125
>> 599.802978516 150.824996948
>> H1.L H1.P H1.W H1.B H1.E H1.J H1.U C13.L C13.P C13.W C13.B C13.E C13.J
>> C13.U vol int stat comment flag0
>> 0 {75.HG11} 1.03960 0.03402 0.08416 ++ {0.0} {} {75.CG1} 21.00886 0.34258
>> 0.60154 ++ {0.0} {} 2.09171414375 0.0213 0 {} 0
>> 1 {75.HG21} 1.04055 0.03307 0.07450 ++ {0.0} {} {75.CG2} 20.65424 0.20240
>> 0.50941 ++ {0.0} {} 1.69693529606 0.0198 0 {} 0
>> 
>> 
>>
>> This is 19 Columns of data.
>>
>> The first line describes what datatypes is to be found in the following
>> lines.
>> Here:
>> Line 1 is the label of nucleus
>> Line 2 is the dataset from where the file is created from
>> Line 3 is the Sweep (Spectral) Width [sw] in Hz
>> Line 4 is the Nuclear magnetic resonance frequency at the given
>> spectrometer field. In MHz.
>>
>> Then follow a line of header description.
>> H1.L must be the label for the H1. Residue 75, proton HG11
>> Then follows .P, .W and .B, which I don't know what it is?
>> The same for, .E, .J and .U.
>> Then comes for carbon C13.
>>
>> Ind the end, there must be the (vol) volume integration intensity and the
>> (int) the top point intensity?
>>
>> For determination of the errors of the intensity, I see that you have 2x
>> duplicated spectra (10ms, and 90ms.)
>> Is this what you wan't? Or do you want to measure the RMSD of the
>> background noise?
>> See:
>> http://wiki.nmr-relax.com/Spectrum_error_analysis
>> http://wiki.nmr-relax.com/RMSD
>>
>> Can you elaborate on:
>> .P, .W and .B
>> or .E, .J and .U. ???
>>
>> 

Re: regarding installation

[Edward d'Auvergne]

Hi Rakesh,

Welcome to the relax mailing lists!  For your problems, it would help
if you reported more of the text from the problems you see.  For
example typing:

$ relax --log log_file

without the prompt symbol "$" should place all output into the file
'log_file'.  If this doesn't work, then there is the option of running
one of:

$ relax > log_file
$ relax >> log_file 2>&1

The text before the reported line numbers is very important for
understanding the problem (as well as those after).  I would also
recommend you try running:

$ relax -i > relax_info.log

And copying and pasting that output into an email as well.  Note that
file attachments have been blocked on these mailing lists.  Normally I
would have said that it is your numpy version which is problematic.
However relax should produce a clean message such as:

$ ./relax
Version 1.5.2 of the 'numpy' dependency is not supported, numpy >= 1.6
is required.
$

Maybe the issue is with your Python version?  Could you please report
the versions of Python, relax, minfx, bmrblib, numpy, and scipy you
are using?

Cheers,

Edward



On 19 April 2016 at 19:39, Rakesh Sharma  wrote:
> Hello Everyone,
> I am new user to relax and having error in installing it on windows. after
> installing when i type relax in CMD i got error in cmd as in
>
>  line 72 of dep_check.py
> if version_comparison(numpy.version.version, '1.6') == -1:
>
> and in line 52
> version1 = [int(val) for val in version1.split('.')]
>
> and errors are
>
> value error:  invalid literal for int<> with base 10: '0b1'
>
>
> can anybody please suggest me the solution. My mail id is
>
> rakeshrocky.phys...@gmail.com
>
> 
> Virus-free.
> www.avast.com
> 
> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Wiki spam bot cleanup.

[Edward d'Auvergne]

Hi,

If no one objects, I might clean up - i.e. permanently delete - all
non-trusted users on the relax wiki:


http://wiki.nmr-relax.com/index.php?title=Special:ListUsers&offset=&limit=500

There are a large number of spam bots sitting there that are blocked
from doing anything, and it would be good to clear them out.  If you
have an account but are not trusted yet, unlikely as most of the
non-trusted users have typical spam bot names, please respond to this
email to have your wiki account trusted.

To improve the wiki user registration process, I have installed the
customUserCreateForm extension:

http://wiki.nmr-relax.com/index.php?title=Special:UserLogin&type=signup
https://www.mediawiki.org/wiki/Extension:CustomUserCreateForm

Well, more like manually created the extension.  I have included a new
text section:

"""
Editing the wiki

To be granted editing access to the relax wiki, please send a message
to the http://www.nmr-relax.com/communication.html#relax-users";>relax-users
mailing list. This is to verify that you are not a spam bot
automatically creating an account. Please include a link to your
research group's website, or equivalent, to help with the verification
process. This measure was taken due to excessive and uncontrollable
spamming of the wiki.
"""

This should significantly clarify the process.

Regards,

Edward

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Re: Confidence in Model-free output

[Edward d'Auvergne]

Hi Jonas,

Welcome to the relax mailing lists!  From the output, I guess you are
using the automated model-free analysis protocol (the one I developed
and published).  Or are you running a custom analysis protocol?  Such
results are not uncommon and are usually an indication of a bigger
problem.  Often this comes back to inadequate temperature calibration
and/or control - have a close look at this text I wrote on the
subject:

http://www.nmr-relax.com/manual/Temperature_control_and_calibration.html

Other times it can be due to a bias in the fitting of relaxation
curves.  Which software did you use to calculate the relaxation rates
from the base data?  Another reason could be the failure of the
diffusion tensor optimisation due to the specific tensor not being an
adequate description of reality.  This happens if you have large scale
internal motions, partial dimerisation (even with 5-10%), long
flexible tails, etc.  A good test is to use the local_tm global model,
which is strangely absent from the above list of global models.  The
local_tm global model will always be too noisy and give some terrible
outlier values, but in general it is a good test for the diffusion
tensor approximation.  As there is no global diffusion assumed, the
local tm values can adapt to the local diffusion contribution.  The
single value may be a good enough approximate average value for the
spread of 3, 5, 10 or more global diffusion coefficients.  Therefore
if you see the same trend in S2 values in the local_tm models as you
do in the oblate spheroid, then you know that the trend is real.
Whether that real trend is due to the protein system or due to bad
input data is another question.  Hopefully this helps.

Regards,

Edward











On 6 January 2016 at 10:14, Jonas Hanske  wrote:
> Hi Edward,
>
> I am a last-year grad student working at a Max Planck Institute in Potsdam, 
> Germany. My thesis is concerned with a Ca2+ binding protein. I collected full 
> set of backbone relaxation data of the apo and holo form at two fields (600 
> and 750) and saw a slight difference in R2 (about 10% decreased in holo 
> form), some difference in R1 (slightly increased in holo form), and no change 
> in NOE. However, after I run model free analysis (using the holo structure 
> for both apo and holo form since no apo structure is available, all 9 
> local_tm models, and all diffusion models), I saw a global tm difference of 
> more than twofold and tremendous changes in s2 values in both forms with up 
> to 50% decrease for the holo form. Is this a likely outcome? I do not know if 
> I should trust model selection especially since the oblate model that was 
> chosen needed about 200 iterations to converge. I used the Newton minimizing 
> method. Below, I copied the AIC output from the console and the corresponding 
> global tm values.
>
> I'd be happy for any advice!
>
> Thanks in advance,
>
> Jonas
>
>
> AIC model selection for apo form
>
> Global model - all diffusion tensor parameters and spin specific model-free 
> parameters.
> # Data pipe  Num_params_(k)
> Num_data_sets_(n)Chi2 Criterion
> sphere - mf (Wed Dec 30 14:23:37 2015)   197   468
>   526.81736920.81736
> prolate - mf (Wed Dec 30 14:23:37 2015)  185   468
>   538.26716908.26716
> oblate - mf (Wed Dec 30 14:23:37 2015)   197   468
>   512.99733906.99733
> ellipsoid - mf (Wed Dec 30 14:23:37 2015)197   468
>   518.69107912.69107
> The model from the data pipe 'oblate - mf (Wed Dec 30 14:23:37 2015)' has 
> been selected.
>
> Global tm = 1.5247e-08 s
>
>
>
> AIC model selection for holo form
>
> Global model - all diffusion tensor parameters and spin specific model-free 
> parameters.
> # Data pipeNum_params_(k)
> Num_data_sets_(n)Chi2  Criterion
> sphere - mf (Tue Jan  5 18:26:27 2016) 206   504  
> 2305.052732717.05273
> prolate - mf (Tue Jan  5 18:26:27 2016)209   504  
> 2299.948082717.94808
> oblate - mf (Tue Jan  5 18:26:27 2016) 209   504  
> 2281.815432699.81543
> The model from the data pipe 'oblate - mf (Tue Jan  5 18:26:27 2016)' has 
> been selected.
>
> Global tm = 6.8584e-09 s
>
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Re: How to make one fit from two experiments

[Edward d'Auvergne]

Hi Jens,

Sorry for not getting back to you earlier.  By searching the relax
directories, I found the files
./test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/acbp_cpmg_disp_048MGuHCl_40C_041223/relax_2_spins.py
and 
./test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/acbp_cpmg_disp_101MGuHCl_40C_041223/relax_2_spins.py.
These may be what you are after and what the tutorial refers to.
Otherwise I would highly recommend looking at the scripts in
sample_scripts/relax_disp/.  Specifically the cpmg_analysis.py script.
This standalone script runs the analysis at two field strengths and
was run on real data (you'll find a copy of the script and data in the
Hansen/ test suite data directory).  I hope this helps.

Regards,

Edward




On 23 December 2015 at 13:22, Jens Fuglsang Ringsholm
 wrote:
> Hey.
>
> i tried to follow the analyse in GUI tutorial:
> http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved
>
> but i cant find the relax_2_spins.py script.
>
> Jens
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Re: How to make one fit from two experiments.

[Edward d'Auvergne]

Hi Jens,

Welcome to the relax mailing lists!  For you question, you may need to
be more specific about which type of experiment, as relax can analyse
data from many different unrelated NMR experiments.  Not only that,
but there are many different types of dynamics analysis that can be
performed on the same data.  For a full list, see:

http://www.nmr-relax.com/features.html

As for how to use relax, I would suggest looking at the relax manual.
For many of the analyses, you'll find step-by-step tutorials for using
relax either via the more commonly used scripting interface, or for
some analyses via the graphical user interface (GUI).  These should
help you get started, and will be sufficient for most analyses.  I
hope this helps.  Don't hesitate to ask if you have any other
questions.

Regards,

Edward




On 18 December 2015 at 12:20, Jens Fuglsang Ringsholm
 wrote:
> Hello
> i am an undergrad student trying to use relax for fitting two experiments 
> with the same protein, at different field strengths. Does relax have an 
> application for this and how do i use it?
>
> Jens Fuglsang Ringsholm
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Re: Experimental: Try relax at Google Cloud Computing

[Edward d'Auvergne]

On 29 November 2015 at 00:46, Troels Emtekær Linnet
 wrote:
> Hi relax users.
>
> I have written a tutorial to get relax running at Google Cloud Computing.
>
> The tutorial can be found here:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing
>
> Consider this as a very experimental procedure.
>
> The Cost of running Google Cloud Computing has been rapidly dropping in
> 2015.
>
> This could be of interest to have access to 32 cores for a limited time, if
> some computations should be performed fast, and no immediately computer
> cluster is available at your facility.
>
> Any comments, hints or tips is appreciated.
>
> Is this a viable and sustainable solution?

Hi Troels,

This sounds like quite a useful service if someone would like to run a
heavy calculation on a cluster when they don't have access to powerful
computing infrastructure.  The instructions at
http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing are very
useful for setting this up.  I would advise though to first run the
calculation on a single core system as a test, to make sure everything
is running smoothly.  The user should carefully check every single
warning.  That would avoid running an incorrectly set up calculation
on the Google Cloud Computing, so that the user doesn't have to re-run
all the calculations a second time.  I think this is quite a good
idea!

Cheers,

Edward

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Re: [bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d'Auvergne]

Hi Martin!

I've now fixed this bug (http://gna.org/bugs/?24131).  Could you
please update your svn copy of the relax trunk (I think I remember you
used this at some point) and check if the code works with your full
results file?

Cheers,

Edward



On 30 November 2015 at 17:47, Edward d  Auvergne
 wrote:
> Update of bug #24131 (project relax):
>
>   Status:   Need Info => Fixed
>  Open/Closed:Open => Closed
>
>
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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 20 November 2015 at 14:17, Troels Emtekær Linnet
 wrote:
> Hi.
>
> My colleagues Kresten Lindorff-Larsen and Amelie Stein kindly helped me find
> some references:
>
> http://zhanglab.ccmb.med.umich.edu/HAAD/
> http://zhanglab.ccmb.med.umich.edu/papers/2009_7.pdf
>
> Fortran code:
> http://zhanglab.ccmb.med.umich.edu/HAAD/haad.f90
>
> http://kinemage.biochem.duke.edu/software/reduce.php
> http://kinemage.biochem.duke.edu/software/readme.reduce.html
> http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/PDFs/1999WordJMB285b.pdf
>
> I don't know the license of the programs, and if they should/could be
> implemented in relax efficiently by
> running the code as external program in the respectively software
> environments.

Hi Troels,

Thanks for digging out those references.  The HAAD algorithm and
software seems promising.  The online server could be used to create a
number of system tests (the check out all different molecule types),
and then the algorithm implemented to exactly match the HAAD software
results.  In the future, maybe we could ask them about dual licensing
a copy under the GPLv3+ licence to allow us to translate the FORTRAN
code directly into Python, as most of this seems to be hardcoded
numbers anyway.  I also cannot find a licence for HAAD, but the last
sentence of their abstract sounds like they intended their code to be
public domain:  "Both an executable and the source code of HAAD are
freely available at http://zhang.bioinformatics.ku.edu/HAAD";.  So
maybe they'll be ok with the dual licensing idea to allow a direct
translation and addition into the relax library (maybe in
/lib/structure/protons/).

For Reduce, we could also do the same, but calculating the results
offline and converting them to system tests.  Then in the
structure.attach_protons user function, we can have the algorithm
parameter which can be set to 'HAAD', 'Reduce', etc., citing the
papers in the user function docstring.  Anyway, I don't have time to
implement these for now, but these are lots of great ideas for future
additions.

Cheers,

Edward

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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 19 November 2015 at 14:55, Alain Oregioni  wrote:
> Hi Edward,
>
> Thank you very much for your reply; I'm glad it's a simple error.  I'll add
> protons to the PDB.
>
> If I may say, it would be nice to have a simple way of doing it in the
> script, even roughly for a start: if it "works" with a sequence, it wouldn't
> be worse to do it with a PDB without H (add any warning necessary in the
> description).

If you'd like to try to hunt down the scientific publications that are
the base reference for the correct placement of protons, that would be
a great start for implementing it.  I searched once but failed.  But
that was under a time constraint, so I ended up using Molmol.  I
didn't like what PyMOL said about its algorithm, it sounds incredibly
un-scientific:

"h_add uses a primitive algorithm to add hydrogens onto a
molecule.", from http://pymolwiki.org/index.php/H_Add

It would be good to have a structure.attach_protons or
structure.add_protons user function so that everything can be
performed in the script.  However in some cases (for example, say in
non-planar aromatic rings), a proper QM, QM/MM, or force field
optimisation may be required for accurate placement.


> Hopefully, things will go smoothly for me from now on...

Well if it doesn't, don't hesitate to ask here.  The mailing list
archives are also an incredibly useful reference:

http://www.nmr-relax.com/communication.html#mailing-lists

The amount of content archived - with both questions and answers - is huge!


> This mailing list is very useful. keep it alive!

It's an open source project, so it can never really die ;)  If you
like the mailing lists, maybe you'd find value in signing up for the
wiki as well ( http://wiki.nmr-relax.com ).  Creating or expanding
articles, or documenting what you do in tutorials can be quite useful
for truly understanding the concepts.  For example a new article on
adding protons to a 3D structure might help with the above ideas.

Regards,

Edward

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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 19 November 2015 at 13:03, Alain Oregioni  wrote:
> Hi Edward,
>
> Thanks for your reply. I was out of the office till now, so I've not had
> time to debug more till now.
>
>  I had a look at the log and I didn't see any warning earlier than the ones
> I mentioned, so I'm again stuck. I will check for name mismatch though, as
> this has happened before.
>
> Sorry about the attachments, I'm afraid I didn't read the communication
> protocols...Here's the beginning of the script:
>
> #
>
> # The diffusion model.
> DIFF_MODEL = 'prolate'
>
> # The model-free models.  Do not change these unless absolutely necessary,
> the protocol is likely to fail if these are changed.
> MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
> LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
> 'tm8', 'tm9']
>
> # The grid search size (the number of increments per dimension).
> GRID_INC = 13
>
> # The optimisation technique.
> MIN_ALGOR = 'newton'
>
> # The number of Monte Carlo simulations to be used for error analysis at the
> end of the analysis.
> MC_NUM = 500
>
> # Automatic looping over all rounds until convergence (must be a boolean
> value of True or False).
> CONV_LOOP = True
>
> # The local paths.
> SEQ_PATH =
> 'C:\\Users\\aoregio\\Desk\\Crick\\Projects\\Woolfson_coiledCoil\\RC'
>
>
> # Set up the data pipe.
> ###
>
> # The following sequence of user function calls can be changed as needed.
>
> # Create the data pipe.
> pipe_bundle = "mf (%s)" % asctime(localtime())
> name = "origin - " + pipe_bundle
> pipe.create(name, 'mf', bundle=pipe_bundle)
>
> # Load the PDB file.
> structure.read_pdb('4DZM-CC-pIL-I17N-dimer-AsnA.pdb', dir='.',
> set_mol_name=['CCDi_mol1','CCDi_mol2'], alt_loc='A')
>
> # Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
> #structure.load_spins(spin_id='@N', ave_pos=False)
> structure.load_spins(spin_id=':6@N', ave_pos=False)
> structure.load_spins(spin_id=':13@N', ave_pos=False)
> structure.load_spins(spin_id=':17@N', ave_pos=False)
> structure.load_spins(spin_id=':20@N', ave_pos=False)
> structure.load_spins(spin_id=':27@N', ave_pos=False)
>
> spin.isotope('15N', spin_id='@N*')
> spin.isotope('1H', spin_id='@H*')
>
> # Generate the 1H spins for the magnetic dipole-dipole relaxation
> interaction.
> sequence.attach_protons()

Hi Alain,

The problem is right here!  The sequence.attach_protons user function
is only for use when you don't have a 3D structure
(http://www.nmr-relax.com/manual/sequence_attach_protons.html).  I
should probably document that better!  Ok, done:

http://article.gmane.org/gmane.science.nmr.relax.scm/25823

You should load your protons from the 3D structure with
structure.load_spins user function calls
(http://www.nmr-relax.com/manual/structure_load_spins.html).  That way
the proton spin containers will have atomic coordinates, and the NH
bond vectors can then be calculated (which you'll need to add to your
script, see http://www.nmr-relax.com/manual/interatom_unit_vectors.html).
For more details, see:


http://www.nmr-relax.com/manual/d_Auvergne_protocol_script_mode_setting_up_the_spin_systems.html

and the following pages.  If you do not have protons in your PDB file,
you'll need to generate them with external software (Molmol, Pymol,
etc.).  Unfortunately I haven't implemented a structure.attach_protons
user function yet, as I never found the citation for an algorithm to
correctly place protons in an X-ray structure.  And I know that the
calculated positions are not always the same for different software
programs, so it would be good to implement a number of the algorithms
so that there is a choice.

Regards,

Edward

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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 12 November 2015 at 19:00, Alain Oregioni  wrote:
> Hi,
>
> I'm new to Relax and I'm having some trouble running a model free analysis
> with my data. In short, all the spins are being deselected, supposedly
> because of missing structural data even though I have loaded a PDB of the
> structure.
>
> Some details of the system:
> I'm using Relax 4.0.0 with scripts under Win7 Pro 64
> The molecule is a homodimer and I have R1, R2, hetNOE data at 600 and 700
> MHz
> The data is only from 5 spins out of 31 (for a chain, both chains being
> identical)
> The pdb is from a crystal structure (so, no proton)
>
> What I've done so far:
> I've run the dauvergne_protocol.py with 'local_tm' and 'sphere' without
> problem. 'sphere' converged after 5 rounds. Both gave 'aic' solutions (but
> then, I think they are not using the PDB directly).
>
> However, when I run any of 'prolate', 'oblate', 'ellipsoid', the script end
> up with "no model selected...'aic' pipe not created".
> Looking at the console output, it seems that after the data is loaded fine
> and dAuvergne_protocol() starts:
> - pipe is created OK
> - local_tm is read OK
> - model_free.remove_tm() is run OK
> - diffusion_tensor.init() is run OK
> - fix()  is run OK
> Then:
> - minimise.grid_search() starts and deselects all the spins: "Over-fit spin
> deselection... because of missing structural data"
> Of course, after this, the grid search does not work.
>
> I'm thinking that my system is far from standard for this type of analysis,
> and there are a few possibilities for things going wrong, starting with the
> fact it's a homodimer, and that the spins with data are in limited numbers
> (although they are spatially well distributed). But I have no ideas
> how/where/why, so I'm a bit stuck for now. Does anyone have an idea?
>
> I've attached a screenshot and the first 3 scripts in case that helps. If
> you need anything else, please ask.


Hi Alain,

Welcome to the relax mailing lists!  Have you managed to work out what
the problem was?  I would suggest looking at your log file (you should
really run relax with the --log or --tee options to capture
everything).  Look at the very top of the log for any warnings.  This
type of error is almost always visible as a warning in the set up
stage of the analysis.  Specifically where the structural data is
loaded into the relax data store.  There is probably a mismatch
between the X and H spins and how they are named in the PDB file.
What are the first few lines of your analysis script?

Note that attachments cause a large strain on the open source
infrastructure, as they are amplified and sent off to everyone on the
mailing list and to the 4 mailing list archives (
http://www.nmr-relax.com/communication.html#relax-users ).  Therefore
attachments will be automatically stripped out of the mailing list
messages.  To send files, the best is to create a bug report (
https://gna.org/bugs/?group=relax ) or support request (
https://gna.org/support/?group=relax ) and attach the files there.


> I've also noticed something that's probably not related, but just in case:
> it seems that the function minimise.grid_search() starts with 'inc=11' even
> if I passed 'GRID_INC=13' in my script (through dAuvergne_protocol() )...If
> it's not expected, and other variables are somehow not updated, this might
> be the cause of the problems.

If you have a look at the auto_analyses/dauvergne_protocol.py file (
http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol-module.html
), you see another option called 'diff_tensor_grid_inc' which defaults
to {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}.  This
is where this number of 11 comes from.  See the file itself for more
details.

Regards,

Edward

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Re: back calculation of relaxation data

[Edward d'Auvergne]

Hi Christina,

I have now fixed the equation in the manual:

 http://svn.gna.org/viewcvs/relax?view=revision&revision=28071

Thank you for reporting the error.  For the
http://wiki.nmr-relax.com/CGS_versus_SI article, hopefully I'll one
day extend this to cover the differences in the equations in the NMR
literature.  As Troels asked, could you give a few more details of
what you'd like to do?  Where does the results.bz2 file come from?
Step-by-step points would be ideal.  If it is from a model-free
analysis, open it in a text editor and see if the back calculated data
is not already there (in most cases it will be).  Are you modifying
some values and then would like new back calculated data?  These are
all important questions for determining how to create a new script
suited for your needs, for example to read in the results.bz2 file,
make the modifications you wish, back-calculate the data, and then
output it into text files.

Regards,

Edward




On 16 November 2015 at 10:33, Christina Möller  wrote:
> Hi Troels,
>
> thanks for your support. I am using the generate_ri.py script to back
> calculate the relaxation data from given s2, s2f, s2s, te, tf, ts values to
> compare it to the original experimental data. I would like to know if it is
> easily possible to read in the parameters for each spin automatically from
> the results.bz2 file (obtained by the full model-free optimisation) or from
> lists, in order to run this script only once.
> So far, I executed the generate_ri.py script seperately for each residue and
> I obtained the back calculated data but this is certainly not the most
> efficient way.
>
> Best,
> Christina
>
>
>
>
>
> Am 11/15/2015 um 06:47 PM schrieb Troels Emtekær Linnet:
>>
>>
>> Dear Christina.
>>
>> I think Edward is on vacation, but maybe I can help.
>>
>> I have only worked on the dispersion part of relax and by no means expert
>> on the model free part.
>>
>> But I understand the data structure of relax and can maybe help with a
>> script for your analysis.
>>
>> Can you provide a description of where you are in the process, and what
>> you aim for.?
>>
>> Best Troels
>>
>> Den 13. nov. 2015 12.12 PM skrev "Christina Möller"
>> mailto:c.moel...@fz-juelich.de>>:
>>
>> Dear Edward,
>>
>> thank you so much for your recommendations and the really helpful wiki
>> article about the CGS and SI unit system. Now I understand the
>> equation
>> differences and successfully back-calculated my relaxation data.
>>
>> Furthermore, I used the generate_ri.py script and the back-calculated
>> values are close to the experimental data (as expected). I have to
>> admit
>> that I copied the motion parameters (s2,sf2,s2s,tf, etc) and the
>> associated model manually into the script and executed the script
>> several times for different residues. I am pretty sure that it is
>> possible to include one or several lists in order to automatically
>> update these parameters for each residue and run this script only one
>> time. Unfortunately, I was not able not find out how this works. Could
>> you give me an idea?
>>
>> Thanks,
>> Christina
>>
>>
>>
>> Am 11/05/2015 um 03:53 PM schrieb Edward d'Auvergne:
>>
>> Hi Christina,
>>
>> Please see below:
>>
>> On 5 November 2015 at 14:05, Christina Möller
>> mailto:c.moel...@fz-juelich.de>> wrote:
>>
>> Dear Edward and relax-users,
>>
>> I am sorry to ask you again for some advice to back
>> calculate the relaxation
>> data from the model parameter values. Here is what I tried
>> so far:
>> For the back calculation I loaded the final results
>> determined by the
>> automated analysis using the dauvergne_protocol.py into
>> the relax gui. Then
>> I selected the back_calc tool from user functions ->
>> relax_data.
>> After starting the back calculation without any entry
>> relax> relax_data.back_calc(ri_id=None, ri_type=None,
>> frq=None)
>> I get the following error message:
>> RelaxWarning: comparison to `None` will result in an
>> elementwise object
>> comparison in the future.
>>
>> This is a warning produced by more recent versions of the
>> numpy Python
>> pa

Re: back calculation of relaxation data

[Edward d'Auvergne]

On 5 November 2015 at 15:53, Edward d'Auvergne  wrote:
> On 5 November 2015 at 14:05, Christina Möller  wrote:
>> I know that the relaxation data can also be back calculated using the
>> equations 7.3a - 7.8 in the relax manual (PDF), although it is not that
>> trivial for an ellipsoid model because I need to determine the weights. Is
>> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of
>> c=2/15(ωN*∆σ)^2 like it can be found in literature?
>
> These two factors come from using CGS vs. SI units.  I have mentioned
> this issue before (see
> http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
> ).  I have also started a stub wiki article to help explain these
> differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units
> the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
> throughout relax.  This has made some parts of relax more difficult to
> implement as there are many equations in the literature in CGS units,
> and the authors will often not identify this older system.  Some
> stubborn people just prefer the magnetic constant to be 1 rather than
> µ0/(4π), and will not shift from the CGS metric system to the SI
> metric system.

Hi Christina,

The wiki article http://wiki.nmr-relax.com/CGS_versus_SI is now
somewhat improved.  However it doesn't cover all of the NMR constants
yet, as that will be a lot of work to derive.  Anyway, I hope that
helps a little to understand the equation differences seen in the NMR
literature.

Regards,

Edward

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Re: back calculation of relaxation data

[Edward d'Auvergne]

Hi Christina,

Please see below:

On 5 November 2015 at 14:05, Christina Möller  wrote:
> Dear Edward and relax-users,
>
> I am sorry to ask you again for some advice to back calculate the relaxation
> data from the model parameter values. Here is what I tried so far:
> For the back calculation I loaded the final results determined by the
> automated analysis using the dauvergne_protocol.py into the relax gui. Then
> I selected the back_calc tool from user functions -> relax_data.
> After starting the back calculation without any entry
> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=None)
> I get the following error message:
> RelaxWarning: comparison to `None` will result in an elementwise object
> comparison in the future.

This is a warning produced by more recent versions of the numpy Python
package.  It is harmless message about changes which will occur in
numpy, and it is safe to ignore.  Note that I have fixed this in the
source code repository and the fix will appear in the future when I
release relax 4.0.1 (it is not present in relax 4.0.0 at
http://wiki.nmr-relax.com/Relax_4.0.0 ).  This was first reported at:

[relax-users] RelaxWarning: comparison to `None` will result in an
elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1839 ).

And the solution at:

[relax-users] Re: RelaxWarning: comparison to `None` will result
in an elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1844 ).


> If I put the frequency in
> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=599468076.0)
> I get another error message
> Traceback (most recent call last):
>  File
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/gui/interpreter.py",
> line 306, in run
>fn(*args, **kwds)
>  File
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/pipe_control/relax_data.py",
> line 132, in back_calc
>spin.ri_data_bc[ri_id] = api.back_calc_ri(spin_index=spin_index,
> ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id])
> KeyError: 'R1_600'
>
> Can you give me a hint what I am doing wrong?

I would suggest using the sample_scripts/model_free/generate_ri.py
sample script.  The relax_data.back_calc user function requires that
the relaxation data ID, the relaxation type, and frequency arguments
be supplied to correctly calculate the desired data (see
http://www.nmr-relax.com/manual/relax_data_back_calc.html ).  Without
this information, relax cannot determine what you would like to do.
Using the sample script would be the easiest option.


> I know that the relaxation data can also be back calculated using the
> equations 7.3a - 7.8 in the relax manual (PDF), although it is not that
> trivial for an ellipsoid model because I need to determine the weights. Is
> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of
> c=2/15(ωN*∆σ)^2 like it can be found in literature?

These two factors come from using CGS vs. SI units.  I have mentioned
this issue before (see
http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
).  I have also started a stub wiki article to help explain these
differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units
the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
throughout relax.  This has made some parts of relax more difficult to
implement as there are many equations in the literature in CGS units,
and the authors will often not identify this older system.  Some
stubborn people just prefer the magnetic constant to be 1 rather than
µ0/(4π), and will not shift from the CGS metric system to the SI
metric system.

Regards,

Edward

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Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 16 October 2015 at 17:42, Sze Chan  wrote:
> Hello Edward,
>
> The problem to load into @N* appears when I use my full data, but using a 
> truncated version does not cause a problem.
>
> I attached, the truncated data, full data, and the PDB I've been using (its a 
> truncated version of a PDB from the RCSB) in the bug report.

Cheers!  I've create a system test and now fixed the problem in relax.
See https://gna.org/bugs/?23933#comment3 .  The problem was introduced
in Nov. 2014.  It might take me a while to release a new version of
minfx, bmrblib, and relax to have all these issues resolved.  Anyway,
you can ignore the comparison to 'None' warnings, as these are
harmless for now.  And they are fixed in minfx, bmrblib, and relax and
so will be part of relax 4.0.1.  With the fixes, the relax log will
look like:


"""
relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)

relax> structure.read_pdb(file='LARA_N_term_no_helixFH_reg.pdb',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)

Internal relax PDB parser.
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb'
for reading.
Adding molecule 'LARA_N_term_no_helixFH_reg_mol24' (from the original
molecule number 24).

relax> structure.load_spins(spin_id='@N', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

# mol_name  res_numres_namespin_num
spin_name
LARA_N_term_no_helixFH_reg_mol24329GLN 1
N
LARA_N_term_no_helixFH_reg_mol24330GLN 10
N
LARA_N_term_no_helixFH_reg_mol24331SER 19
N

relax> structure.load_spins(spin_id='@H', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

# mol_name  res_numres_namespin_num
spin_name
LARA_N_term_no_helixFH_reg_mol24330GLN 0
H
LARA_N_term_no_helixFH_reg_mol24331SER 0
H

relax> structure.load_spins(spin_id='@NE1', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

RelaxWarning: No spins matching the '@NE1' ID string could be found.

relax> structure.load_spins(spin_id='@HE1', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

RelaxWarning: No spins matching the '@HE1' ID string could be found.

relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600402816.0,
file='r1_600.txt',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3,
sep=None, spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt'
for reading.
Traceback (most recent call last):
  File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py",
line 499, in test_bug_23933_relax_data_read_ids
self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1',
frq=600402816.0, file='r1_600.txt', dir=path, res_num_col=1,
data_col=2, error_col=3)
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 925, in read
pack_data(ri_id, ri_type, frq, values, errors,
mol_names=mol_names, res_nums=res_nums, res_names=res_names,
spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 773,
in pack_data
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
RelaxMultiSpinIDError: RelaxError: The spin ID
'#LARA_N_term_no_helixFH_reg_mol24:331' corresponds to multiple spins,
including '#LARA_N_term_no_helixFH_reg_mol24:331@N' and
'#LARA_N_term_no_helixFH_reg_mol24:331@H'.
"""


The bug that was hidden from you in the GUI will now stop relax and
pop up a RelaxError dialog.  Therefore you don't need the new relax
version or use a checked out copy of the source code repository
(unless you'd like the new code to remove all of the numpy
FutureWarning messages).  You just need to set the spin_id argument to
'@N'.  This allows relax to understand that you have nitrogen and not
proton relaxation data - relax will accept both and it is currently
ambiguous if it is 'N' or 'H' data.  Anyway, thank you for the bug
report and attached files.  This has allowed me to fix both the numpy
FutureWarning and missing 'ids' variable problems.  If you see any
other strange warnings or errors, it would be appreciated if you could
report them so that they can be resolved for future relax versions.

Cheers,

Edward

__

Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 11 October 2015 at 19:32, Sze Chan  wrote:
> RelaxWarning: comparison to `None` will result in an elementwise object 
> comparison in the future.

Hi Sam,

This warning is due to something called a FutureWarning which was
introduced into numpy >= 1.9.  It looks like the numpy would like to
change how '==' operates on their numpy arrays.  So the previous relax
code was of the form:

if vector == None:

This used to work and was good for checking if we had set a value.
However the numpy people would like us to now instead use:

if vector is None:

I am running the test suite now with Python 3.5 and numpy 1.9.2, using:

$ python3.5 relax -x -d --tee test_suite.log --traceback

That way I can find all such warnings and replace '==' with 'is' and
silence them all.  However as I mentioned in the other email, this is
not the problem you are having with the analysis.  Thanks for pointing
it out though, the fixes I'll make here will allow relax to continue
running with future numpy versions.

Cheers,

Edward

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Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 12 October 2015 at 09:04, Edward d'Auvergne  wrote:
> On 11 October 2015 at 19:32, Sze Chan  wrote:
>> Hello,
>>
>>
>> While I was setting up my modelfree analysis in the GUI automated protocol , 
>> I received the error in the controller:
>>
>>
>> RelaxWarning: comparison to `None` will result in an elementwise object 
>> comparison in the future.
>>
>>
>> After loading my data, setting dipolar interactions, setting CSA relaxations 
>> and setting the isotopes but before execution of the analysis.
>>
>>
>> I'm not sure what happened to cause the warning, but when the modelfree 
>> analysis is running, each successive round of optimization in each model 
>> does not compare to the previous round, instead it would always compare each 
>> optimized chi-square value to 'none' such as in round 21 of the oblate model:
>>
>>
>> Storing the optimisation results for the spin 
>> '#LARA_N_term_no_helixFH_reg_mol24:358@N', the optimised chi-squared value 
>> is lower than the current value (283.50425283 < None).
>>
>>
>> Even though I'm guessing it should refer to a previously optimised value?
>>
>>
>> During the analysis it would go through the default 30 rounds of 
>> optimisation for each global model but not reach convergence.
>>
>>
>> I was wondering how I can remedy this or at least create a log file so I can 
>> make my problem more clear.
>
> Hi Sam,
>
> I would suggest running relax with these options:
>
> $ relax --gui --log relax_warning.log --traceback
>
> This will start the GUI, send all output into a 'relax_warning.log'
> file, and produce highly detailed RelaxError and RelaxWarning messages
> pointing to the exact place in the code where the problem occurred.
> Then exit relax once this warning first occurs (using kill if
> necessary).
>
> Which version of relax are you using by the way?  And which numpy
> version?  The RelaxWarning message you see is either due to Python or
> numpy (specifically using newer versions).  I have seen it many times
> before, and I try to avoid it in the code where possible.  Strangely I
> have never seen this one before.  The relax test suite tests the full
> automated dauvergne_protocol analysis, including multiple rounds of
> optimisation and convergence tests.  And for each relax release I run
> the full test suite on Python version 2.5, 2.6, 2.7, 3.0, 3.1, 3.2,
> 3.3, and 3.4 (and now 3.5).  Because the test suite has not replicated
> the problem you see, maybe it has something to do with numpy.  Anyway,
> I look forward to seeing the traceback on that RelaxWarning, and maybe
> the output of 'relax -i'.  If you'd like to attach files, then please
> create a bug report and attach the file to the report (
> https://gna.org/bugs/?func=additem&group=relax ).

Hi Sam,

Thanks for creating the bug report ( https://gna.org/bugs/?23933 ).
From this I can see that the RelaxWarning is not the problem, but
rather this:

"""
relax> relax_data.read(ri_id='R1_600_2', ri_type='R1',
frq=600402816.0, file='C:\\Users\\Sam Chan\\Desktop\\r1_600.txt',
dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1,
res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None, spin_id='@N*')
Opening the file 'C:\\Users\\Sam Chan\\Desktop\\r1_600.txt' for reading.
Traceback (most recent call last):
  File "C:\relax\gui\wizards\wiz_objects.py", line 166, in _apply
self.exec_status = self.on_execute()
  File "C:\relax\gui\uf_objects.py", line 917, in on_execute
return_status = self.execute(self.name, **kargs)
  File "C:\relax\gui\uf_objects.py", line 839, in execute
return_status = interpreter.apply(uf, *args, **kwds)
  File "C:\relax\gui\interpreter.py", line 109, in apply
fn(*args, **kwds)
  File "C:\relax\pipe_control\relax_data.py", line 920, in read
pack_data(ri_id, ri_type, frq, values, errors,
mol_names=mol_names, res_nums=res_nums, res_names=res_names,
spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id)
  File "C:\relax\pipe_control\relax_data.py", line 767, in pack_data
if ids:
NameError: global name 'ids' is not defined
"""

Did you see this error in the GUI?  To help debug this, I was
wondering if you could attach a shortened version of the r1_600.txt
file (truncated to 1 or 2 residues, but still enough to trigger the
error).  I could then use this to create a new system or GUI test to
catch the problem.  That will allow me to come up with a fix in
normally a few minutes.  Oh, you may have seen that I just released
relax 4.0.0, the first of the 4 series (
http://wiki.nmr-relax.com/Relax_4.0.0 ).  However this problem you see
will still be present.

Cheers,

Edward

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Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 11 October 2015 at 19:32, Sze Chan  wrote:
> Hello,
>
>
> While I was setting up my modelfree analysis in the GUI automated protocol , 
> I received the error in the controller:
>
>
> RelaxWarning: comparison to `None` will result in an elementwise object 
> comparison in the future.
>
>
> After loading my data, setting dipolar interactions, setting CSA relaxations 
> and setting the isotopes but before execution of the analysis.
>
>
> I'm not sure what happened to cause the warning, but when the modelfree 
> analysis is running, each successive round of optimization in each model does 
> not compare to the previous round, instead it would always compare each 
> optimized chi-square value to 'none' such as in round 21 of the oblate model:
>
>
> Storing the optimisation results for the spin 
> '#LARA_N_term_no_helixFH_reg_mol24:358@N', the optimised chi-squared value is 
> lower than the current value (283.50425283 < None).
>
>
> Even though I'm guessing it should refer to a previously optimised value?
>
>
> During the analysis it would go through the default 30 rounds of optimisation 
> for each global model but not reach convergence.
>
>
> I was wondering how I can remedy this or at least create a log file so I can 
> make my problem more clear.

Hi Sam,

I would suggest running relax with these options:

$ relax --gui --log relax_warning.log --traceback

This will start the GUI, send all output into a 'relax_warning.log'
file, and produce highly detailed RelaxError and RelaxWarning messages
pointing to the exact place in the code where the problem occurred.
Then exit relax once this warning first occurs (using kill if
necessary).

Which version of relax are you using by the way?  And which numpy
version?  The RelaxWarning message you see is either due to Python or
numpy (specifically using newer versions).  I have seen it many times
before, and I try to avoid it in the code where possible.  Strangely I
have never seen this one before.  The relax test suite tests the full
automated dauvergne_protocol analysis, including multiple rounds of
optimisation and convergence tests.  And for each relax release I run
the full test suite on Python version 2.5, 2.6, 2.7, 3.0, 3.1, 3.2,
3.3, and 3.4 (and now 3.5).  Because the test suite has not replicated
the problem you see, maybe it has something to do with numpy.  Anyway,
I look forward to seeing the traceback on that RelaxWarning, and maybe
the output of 'relax -i'.  If you'd like to attach files, then please
create a bug report and attach the file to the report (
https://gna.org/bugs/?func=additem&group=relax ).

Cheers,

Edward






>
>
> Sam
> ___
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Re: Model free on symmetric homodimer, problems with grace plots

[Edward d'Auvergne]

On 7 October 2015 at 09:43, Panwalkar, Vineet  wrote:
> Hello Edward and relax users,
>
> I have been recently using relax to carry out model free analyses on two 
> different states of my protein at 600 and 800 MHz. I am working with a LOV 
> domain (132 residues) which exists in a ground "dark" state and a photoactive 
> "light" state. Both states exist as a symmetric homodimer in solution. For 
> the analysis I have been using the crystal structures, one monomer at a time. 
> Also, the resonances showing overlap have not been included in the analyses. 
> There is no difference in the backbone as such between the two crystal 
> structures. Along with model-free I have also carried out reduced spectral 
> density mapping. The J(0)s of both the states agree well between the two 
> fields. Hence there is nothing wrong with the data as such. Also both the 
> J(w) agree well with my het-NOE and R1 with respect to regions in the protein 
> showing fast timescale backbone motion.
>
> The model free analysis of the "dark" state goes fine. The S2 values show 
> same regions having fast timescale motions as observed from the raw 
> relaxation data and rSDM. Both the monomers individually give me 
> approximately comparable results. For e.g., a loop between residues 100 and 
> 110 shows flexibility on fast time scale according to the raw data, rSDM as 
> well as relax S2 values.
>
> However, for the "light" state the results from model free appear quite 
> bizarre for both the monomers. The average S2 for the "dark" state was ~ 0.8. 
> As per my raw data and rSDM, I expected the S2 values to be slightly elevated 
> in "light" state. However, my "light" state S2 values are on an average 0.17! 
> Also the same loop is now with higher than average S2 values in the "light" 
> state whereas the raw data and rSDM showed the loop to be flexible, albeit 
> less flexible compared to the "dark" state. The internal motions (Te) are 
> less than 5 ps and seen only in 7 residues. No Ts or Tf. I have attached 
> figures from the spectral density mapping as well as the "dark" and "light" 
> state S2 values to illustrate better what I am trying to say.
> Also, I repeated the "dark" state model free analysis with "dark" state 
> structures. thinking that there might be some bug somewhere and got results 
> just like earlier. But not with the "light" state. Since the backbones 
> between two states are near identical, I used the "dark" state structure to 
> run with relax on the "light" state data. I again get these bizarre results. 
> I am about to run model free with "light" state structure and "dark" state 
> relaxation data. However, I am not sure where the problem lies, whether it is 
> the structure, my data or some bug somewhere. Since the J(0)s add up nicely, 
> I do not think it is the data. It is unlikely that it is bug since the "dark" 
> state ran fine. It is also unlikely that the structure is strange since dark 
> and light states have near identical backbones and there are no missing 
> residues in either of the structures. I must also add that the correlation 
> time obtained from relax are actually comparable with the ones extracted from 
> R2/R1 ratio for both the "dark" and the "light" states. It is only the motion 
> parameters which are weird for the "light" state.
>
> Has anyone encountered something like this recently? Any help/advice here 
> will be very helpful. At this moment the data is only with two fields but I 
> do plan to run relaxation at 900 MHz and use the three fields for model-free 
> as soon as I get time on the magnet.

Hi Vineet,

One thing you must consider is if the approximation of a single
ellipsoidal diffusion tensor is reasonable for the system.  Sometimes
this is not the case.  For example if the single rigid body assumption
is violated, if the dimerization is not 100%, or there are long
flexible tails (breaking the 'free' rigid body assumption).  If you
have been using the model-free analysis protocol I came up with in:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. ( http://dx.doi.org/10.1039/b702202f )

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133. (
http://dx.doi.org/10.1007/s10858-007-9213-3 )

then there is a good check you can perform.  Compare the final results
to the results of the local tm global model.  The local tm model is
almost always over fit, hence the balance of variance vs. bias will be
tipped in the direction of variance (it will be noisy).  However the
local tm global model will have a lot less bias.  In practical terms,
this means that the model will not be affected by the assumption of a
global diffusion tensor (note that it is however affected by the
assu

Re: weights of diffusion

[Edward d'Auvergne]

On 8 September 2015 at 12:40, Christina Möller  wrote:
> Dear Edward and relax users,
>
> I would like to know the weights (ci) of an ellipsoidal diffusion. It
> can possibly be extracted by the weights.py script. Unfortunately, I
> could not find out how to use this script and which input files are
> needed. Can anyone give me a hint how to obtain the weights?

Hi Christina,

Which version of relax are you using?  There is no weights.py script,
however you may be referring directly to the relax source code itself
(at http://www.nmr-relax.com/api/3.3/lib.diffusion.weights-module.html
and http://www.nmr-relax.com/api/3.3/lib.diffusion.weights-pysrc.html
).  These weights are physical constants as derived and presented in
the original papers of Perrin 1934
(http://dx.doi.org/10.1051/jphysrad:01934005010049700 ) and Perrin
1936 http://dx.doi.org/10.1051/jphysrad:01936007010100 ).  There are
written in French, but I have included these in the relax manual at
http://www.nmr-relax.com/manual/The_weights_of_the_ellipsoid.html .
From these equations, you should be able to calculate the weights
yourself.  Note that they are dependent on the XH bond vector
orientation, specifically their projection onto the diffusion tensor.
It will probably be easier to calculate these yourself for each data
point, rather than using the relax code.  If you would prefer to use
the relax code, and know Python scripting, then you'll need to create
2 data containers (class instances) with the appropriate data,
pre-calculating the vector projection onto the diffusion tensor
(data.dx, data.dy, data.dz in the code) and passing these containers
into the lib.diffusion.calc_ellipsoid_ci() function.  I hope this
helps.

Regards,

Edward

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Re: Problems Loading PDB

[Edward d'Auvergne]

Hi Dave,

Sorry for the delayed response, I have just returned from holidays.
Please see below:


On 4 June 2015 at 17:02, Lawrence David Finger  wrote:
> I posed these questions some time ago, but I have not heard from anyone or 
> whether my message was accepted by the moderator. I guess I am not on the 
> list. Below is what I wrote initially.

I just checked the mailing list backend, and your d.finger email
address is not present.  You should try subscribing again.  One step
that is often forgotten is that after you receive the subscription
request email and follow the link, you have to in that page
specifically select to subscript or ignore the subscription.  In most
cases when you are not subscribed, the mailing list maintainer Chris
MacRaild will see your message and accept it.  One problem though is
that public mailing lists are a massive magnet for spam.  So if your
message is buried in a pile of 1000 spam messages, it is sometimes not
seen and thrown out with the 1000 junk messages.  Being subscribed to
the list avoids this.


> We have a question concerning our results from our latest calculations using 
> relaxGUI. We have fed the program NMR relaxation data at 500 and 600 MHz on 
> the free protein and a structure of the protein in complex with DNA from an 
> X-ray structure. We know that binding of DNA induces some secondary 
> structures because the free protein has sections missing in the pdb. Because 
> the free protein structure has residues missing presumably due to disorder in 
> the crystal, we chose to use the structure of the bound protein. Could the 
> use of a structure of our protein with more order than expected cause 
> problems with the selection of the rotational diffusion tensor?

Very much so!  If there is a conformational change, you should
probably split the protein in 2 and analyse each domain or rigid body
separately.


> The diffusion tensor the program has selected doesn’t seem to match the 
> overall shape of the protein. If it can cause a problem, how do I add the 
> residues missing from the crystal structure for the refinement? Furthermore, 
> can the program handle some residues missing in crystal structures?

The problem with a non-spherical model-free analysis is that the
average XH bond vector orientation in solution is a core requirement
of the theory.  If this is incorrect, this can lead to either of the
two well known artefacts:

- Artificial nanosecond motions (the Schurr 1994 paper).
- Artificial Rex value (the Tjandra 1995 paper).

See my 2007 Mol. Biosyst. paper at http://dx.doi.org/10.1039/b702202f
for a review about this problem and how this relates to the under or
overestimation of the vector projection within the diffusion tensor.

One way to handle this situation is to use what I have termed a
'hybrid' model.  For residues which have no structural information,
you can use the local tm model and avoid a global correlation time,
and linearly combine these models with the global diffusion tensor
models applied to all known residues.  You could even shift residues
with high beta factors from the global Brownian diffusion model into
the 'local tm' model category.  relax will allow you to do this, but
it will require a bit of manual work.  So if you know you have two
domains with large structural rearrangements, you can perform three
analyses:

- Local tm for missing residues.
- The full protocol for domain 1.
- The full protocol for domain 2.

Then combine the final results as one model.  There should be zero
overlap of residues in these 3 divisions.  You could then compare
this, using AIC values to take parsimony and non-nested model
differences into account, to a local tm model for all residues.  Note
that the local tm models are generally quite noisy if data from < 3
fields are used.  I hope this helps.

Regards,

Edward

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Re: fixed tm values

[Edward d'Auvergne]

Hi Christina,

Welcome to the relax mailing lists!  As Troels mentioned, I have been
on holidays so can only now reply.  For details, please see below:

On 3 June 2015 at 14:32, Christina Möller  wrote:
> Dear Edward and relax users,
>
> I successfully performed the dauvergne_protocol.py analysis scripts to
> determine the ps - ns dynamics of a 14 kDa protein. The global
> correlation time tm is 9.6 ns.

This value does not seem unreasonable.

> Since other methods suggested a smaller
> global correlation time tm,

Which other methods have you used?  You should note the following issues:

- It is well known that MD underestimates the global correlation time
by about half and David Case is actively researching this area.
- Stoke's law and the related hydrodynamic beads model from Garcia de
la Tor are reasonable for estimating tm for isolated molecules.
However with the super high concentration in NMR samples, these tend
to underestimate the tm value by about half as they do not take
micro-viscosity into consideration.
- ORD measurements as well, as the tm changes between the lower
concentration optical spectroscopic sample and the NMR sample by about
a factor of 2 (micro-viscosity effects being a major factor again).


> I would like to know whether it is possible
> to fix the tm value in all rounds of individual model-free
> optimisations?

As Troels pointed out, this is of course possible.  You can take, for
example, the sample_scripts/model_free/diff_min.py script.  This
already implements a lot of what Troels described for you.  Note
however that this needs to be executed iteratively until the global
chi-squared value between iterations is identical.  See figure 2 of:

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133. (
http://dx.doi.org/10.1007/s10858-007-9213-3 ).

This global iterative optimisation of the diffusion tensor is
essential, and you'll find it documented in Mandel et al., 1995 as
well as in the papers by the Dasha authors.  It will take between 5-20
iterations to properly converge (in rare cases it can be 2 iterations,
in others >50).  For more details, you really should read:

How to get model free parameters from output files (
http://thread.gmane.org/gmane.science.nmr.relax.user/1375/focus=1378
).

This requires an initial diffusion tensor estimate.  And as I
demonstrated in the above paper - as well as first shown in the
Korzhnev et al., 1999 bacteriorhodopsin fragment paper (
http://dx.doi.org/10.1023/a:1008356809071 ) - if this is too far off,
the global minimum will never be reached.  You can however directly
compare the two results using AIC values (not chi-squared values as
the individual model-free models for each residue will be different
and the effects of parsimony will not be taken into account).  An
additional thread which might be of interest is:

AIC to select diffusion model (
http://thread.gmane.org/gmane.science.nmr.relax.user/885/focus=891 ).

There are plenty of other relax-users mailing list threads on the
subject which you can search for at:

http://dir.gmane.org/gmane.science.nmr.relax.user


> The corresponding chi2 values might then be useful to
> evaluate the global correlation times that I obtained by different methods.

Note that you should compare the chi-squared values from the same
program, just to be sure.  Also note that the spherical angle and
Euler angle notations in Modelfree4, Dasha, Tensor2 and relax are not
compatible.  The problem is that the definitions of these angles are
not documented (except in relax) so if you take a diffusion tensor
from one and input it into another, you will see the angles swing
around wildly with the global iterative diffusion tensor estimate
until it converges to the same tensor but with the different angles
(except when a local minimum is hit).  There are 2406 Euler angle
conventions and symmetries for diffusion tensors!

One last thing to note is that relax is extremely flexible in what it
can do.  Using specially designed scripts, relax can replicate the
results of Modelfree4, Dasha, Tensor2, or DYNAMICS.  One exception is
that relax uses a real optimisation constraint algorithm (the
augmented Lagrangian or method of multipliers,
https://en.wikipedia.org/wiki/Augmented_Lagrangian_method ,
https://gna.org/projects/minfx/ ) which the other model-free softwares
do not, hence there can be cases where relax does not find exactly the
same result as the other softwares.

I hope all this information helps.  You should also consider Troels'
suggestion of the dx.map user function to see the diffusion tensor
parameter space (or 3D subsets of it).  I used this in figure 6 of:

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models I. Minimisation algorithms and their performance within
the model-free and B

Re: using relax on supercomputer

[Edward d'Auvergne]

Hi Lora,

I was wondering if you could resend the message that Troels is talking
about, as it missed the mailing list.  Troels has added a link to
http://thread.gmane.org/gmane.science.nmr.relax.user/1821 to link to
the information you provided, but unfortunately it is absent from the
thread and archives.  To keep the thread structure intact, could you
copy and paste the text and then reply to the original email?  That
will preserve the thread structure in the above link.  Having this
information in the mail archives would be greatly appreciated.

Cheers!

Edward


On 29 May 2015 at 18:55, Troels Emtekær Linnet  wrote:
> Hi Lora.
>
> Thank you for your detailed message.
>
> I believe this will help alot of other people, including me. :-)
>
> I took the liberty to write a little post about on the relax wiki.
> http://wiki.nmr-relax.com/OpenMPI#Setting_up_relax_on_super_computer_Beagle2
>
> I hope it comes of use for someone.
>
> Thanks again!
>
> Best
> Troels
>
>
> 2015-05-29 11:46 GMT+02:00 Troels Emtekær Linnet :
>
>> Dear Lora.
>>
>> I am interested in achieving the same thing on our small local computer
>> cluster.
>>
>> I have read from
>> http://beagle.ci.uchicago.edu/using-beagle/
>>
>> That you use Torque to submit jobs.
>>
>> Have you succeeded in getting this to work with relax?
>>
>> Best
>> Troels
>>
>>
>>
>> 2015-05-15 19:52 GMT+02:00 Lora Picton :
>>
>>> Hi,
>>>
>>> I'm working with the administrators of the super computer on UChicago's
>>> campus (Beagle2) to get relax running on their system.
>>>
>>> Because of the way that their system is set up, I will need to have my
>>> data and script files in one directory and submit my job and instructions
>>> to a queue. I can't use the gui version to implement the full analysis.
>>>
>>> I have two questions about doing this.
>>> 1. Can I use the GUI to set everything up and then instead of starting
>>> it, save the scripts so that I can direct them to be started in the queue,
>>> or do I have to modify each script with a text editor?
>>>
>>> 2. When starting the full analysis with a script UI mode (which I need to
>>> do to submit the job), the manual says you need 6 scripts, one for each
>>> diffusion model. Does this mean that I will need to submit multiple jobs to
>>> a queue, one for each model? If yes, would the first 5 need to be done
>>> before the "final" is used? Or would it be possible to direct all of them
>>> to occur in one large script?
>>>
>>> Thanks for any input you might have!
>>> Lora Picton
>>> ___
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>>>
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>>> relax-users@gna.org
>>>
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>>> reminder, or change your subscription options,
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>>>
>>
>>
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Re: using relax on supercomputer

[Edward d'Auvergne]

Hi Lora,

Please see below:

> I have two questions about doing this.
> 1. Can I use the GUI to set everything up and then instead of starting it, 
> save the scripts so that I can direct them to be started in the queue, or do 
> I have to modify each script with a text editor?

Yes, just save the state and then create a basic script that loads
that state and then execute the auto-analysis.  You just need a
pipe.create user function call and the last line of the
dauvergne_protocol.py sample script (and an import from the top).  It
can all be done in a 3 line script, if you wish.


> 2. When starting the full analysis with a script UI mode (which I need to do 
> to submit the job), the manual says you need 6 scripts, one for each 
> diffusion model. Does this mean that I will need to submit multiple jobs to a 
> queue, one for each model? If yes, would the first 5 need to be done before 
> the "final" is used? Or would it be possible to direct all of them to occur 
> in one large script?

This is optional for the auto-analysis, see the diff_model argument:

http://www.nmr-relax.com/api/3.3/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html#__init__

You should use this documentation to help set up the auto-analysis in
script mode.

Regards,

Edward

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Re: Problems Loading PDB

[Edward d'Auvergne]

Hi Ian,

Welcome to the relax mailing lists!  For this problem, it is just
relax not knowing which of the alternate coordinates in the PDB file
to use.  See altLoc at
http://www.nmr-relax.com/api/3.3/lib.structure.pdb_read-module.html#atom
(this is a copy of the PDB standard).  This is usually only for side
chains anyway, and it is generally safe to set it to 'A'.  It is a
character which starts at 'A', so you will find in column or position
17 of the PDB file 'A' and 'B' for some atoms (sometimes 'C' and even
'D', though more is rather rare).  I have deliberately not set the
default to 'A', just in case someone encounters a file with alternate
coordinates.  Then you can look at the PDB file and determine which,
if any, of the coordinates should be used.  For a model-free analysis,
if altLoc is set for the backbone N or H, deselecting the residue
might be the best strategy.  But it is up to you to determine what the
best approach for this PDB file is.  If you have any other issues,
please don't hesitate to ask!

Regards,

Edawrd


On 27 April 2015 at 19:16, Ian A Bennet  wrote:
> Hello,
>
> We are new relax users and are struggling to load structural information
> for each residue.  We have tried loading a pdb file (attached) generated by
> Pymol after proton addition, however we get this error:
>
> RelaxError: Multiple alternate location indicators are present in the PDB
> file, but the desired coordinate set has not been specified.
>
> When we set the "alternate location indicator" to any number (I have no
> clue which number it should be set to) it says the structure is loaded, but
> when trying to extract the atomic positions it spits out an error about no
> positional information could be found.
>
> Is there some sort of easy format that PDB files should be in so that relax
> can extract the information from them?
>
> Many thanks,
>
> Ian.
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Re: question about final files generated

[Edward d'Auvergne]

Hi Lora,

If you have your log messages saved to file (using the --log or --tee
options), then you'll see the model selection messages close to the
end.  You can also load the final relax state file and run the
diffusion_tensor.display user function to see something like:

"""
relax> diffusion_tensor.display()
 __

  Diffusion type   spheroid
  tm (s)   9.08889e-09
  Diso (rad/s) 1.83374e+07
  Da (rad/s)   7.13232e+06
  Dpar (rad/s) 2.30923e+07
  Dper (rad/s)   1.596e+07
  Dratio   1.44689
  theta (rad)  0.96817
  phi (rad)2.47883
  Fixed flag   True
 __
"""

As for the model-free model for each residue, this can be saved to a
file via the value.set user function where the param argument is set
to 'model'.  This is deliberately not performed by default as a
concious design decision.  The reason is because historically there
has been too much emphasis on the specific model selected, whereas the
emphasis should be rather on the dynamics.  The functional
significance of the model-free motions is revealed by the dynamics
itself rather than which model was selected.  As there is a lot of
nesting in the model-free models, and just because a model with no Rex
has been selected does not mean that there is no Rex, just that no
statistically significant Rex can be found with the current relaxation
data.  And sometimes two nested models can be equally good via
standard parsimony-based statistics (AIC for example) and which one is
chosen will be close to arbitrary.  Careful post analysis,
meticulously checking all data, will reveal a number of these cases.
The more complex model will be noisier and its additional parameter
will be on the baseline of statistical significance for that
parameter, below which that parameter is invisible (it could still
exist).  The simpler model is less noisy and the additional parameter
is then considered part of the invisible region - whether or not it
exists can never be determined.  All model-free parameters have such
statistical invisibility bands within the parameter space, where 2
times the lower error bar will hit the zero-intercept.  This is why
de-emphasising models is a good idea.  If you were to remeasure the
relaxation data with higher precision, the dynamics picture will
simply become less noisy and you'll be able to see more into the
invisible parameter regions.  However the model selection picture will
change radically.  Anyway, just run the value.set user function to
obtain the models selected (or look inside the XML state file).

Regards,

Edward


On 13 April 2015 at 23:01, Lora Picton  wrote:
> Hi,
>
> Is there a file in the final results that says which model that each residue 
> fits best to, and which of the overall models of the molecule (sphere, 
> ellipsoid etc) was the best fit?
>
> Thanks for your help.
>
> Sincerely,
> Lora Picton
> ___
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>
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> relax-users@gna.org
>
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Re: relax gui - window resize issue

[Edward d'Auvergne]

Hi Lora,

I have now fixed the problem in relax:

http://article.gmane.org/gmane.science.nmr.relax.scm/25573

I'll probably soon make a minor release of relax 3.3.8 containing just this fix.

Regards,

Edward



On 31 March 2015 at 18:37, Lora Picton  wrote:
> Hi Edward,
>
> Yes, this has fixed the problems.
>
> Thank you so much for your quick response.
>
> Sincerely,
> Lora Picton
> 
> From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of 
> Edward d'Auvergne [edw...@nmr-relax.com]
> Sent: Tuesday, March 31, 2015 2:31 AM
> To: Lora Picton
> Cc: relax-users@gna.org
> Subject: Re: relax gui - window resize issue
>
> Hi Lora,
>
> Welcome to the relax mailing lists!  For the problem you are seeing,
> do you mean that the spin viewer window (i.e. via the main menu
> View->Spin Viewer) cannot be resized?  Or the spin loading wizard when
> clicking on the 'Load spins' button or selecting 'Load spins' from the
> right-click popup menus?  The spin viewer window is designed to be
> resizeable.  However the spin loading wizard needs to be of fixed size
> to allow the user function contents to be packed consistently.  The
> wizard is fixed to the size of 1000x800 (see
> http://www.nmr-relax.com/api/3.3/gui.spin_viewer.frame-pysrc.html#Spin_view_window.load_spins_wizard).
> What is your screen resolution?  Try opening the
> gui/spin_viewer/frame.py file in a text editor and changing size_y
> value from 800 to 750 on the line:
>
> # Initialise a wizard.
>self.wizard = Wiz_window(parent=self, size_x=1000, size_y=800,
> title="Load spins")
>
> Does this solve the problem?  I've normally set a maximum size limit
> of 1000x750 for all fixed sized windows to allow for all standard
> screen sizes, but I can now see two places where this rule has been
> broken.  The lowest resolution I've seen used for relax is 1024x768.
> So if you have this resolution, the height of 750 should hopefully fix
> the problem.  You can find the other problematic window by typing the
> following in the relax root directory:
>
> $ grep -r "Wiz_window(" gui/
>
> If the height of 750 fixes the problem for you, I'll change the values
> in the code.
>
> Cheers,
>
> Edward
>
>
>
>
> On 30 March 2015 at 22:10, Lora Picton  wrote:
>> Hi,
>>
>> I have relax running on my Ubuntu 12.04 laptop, and am running into a 
>> problem with the GUI. When trying to set up spin systems, the spin loading 
>> page is unable to be resized, and the buttons at the bottom are not visible, 
>> and thus not clickable.
>>
>> I have tried playing with the resolution and screen sizes on my display, but 
>> this did not solve the problem.
>>
>> Is there a way to make this window either a smaller, fixed size? 
>> Alternately, is there a way to add the ability to resize the window?
>>
>> Thank you so much for your time and attention.
>>
>> Sincerely,
>> Lora Picton
>> ___
>> relax (http://www.nmr-relax.com)
>>
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>> relax-users@gna.org
>>
>> To unsubscribe from this list, get a password
>> reminder, or change your subscription options,
>> visit the list information page at
>> https://mail.gna.org/listinfo/relax-users

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Re: relax gui - window resize issue

[Edward d'Auvergne]

Hi Lora,

Welcome to the relax mailing lists!  For the problem you are seeing,
do you mean that the spin viewer window (i.e. via the main menu
View->Spin Viewer) cannot be resized?  Or the spin loading wizard when
clicking on the 'Load spins' button or selecting 'Load spins' from the
right-click popup menus?  The spin viewer window is designed to be
resizeable.  However the spin loading wizard needs to be of fixed size
to allow the user function contents to be packed consistently.  The
wizard is fixed to the size of 1000x800 (see
http://www.nmr-relax.com/api/3.3/gui.spin_viewer.frame-pysrc.html#Spin_view_window.load_spins_wizard).
What is your screen resolution?  Try opening the
gui/spin_viewer/frame.py file in a text editor and changing size_y
value from 800 to 750 on the line:

# Initialise a wizard.
   self.wizard = Wiz_window(parent=self, size_x=1000, size_y=800,
title="Load spins")

Does this solve the problem?  I've normally set a maximum size limit
of 1000x750 for all fixed sized windows to allow for all standard
screen sizes, but I can now see two places where this rule has been
broken.  The lowest resolution I've seen used for relax is 1024x768.
So if you have this resolution, the height of 750 should hopefully fix
the problem.  You can find the other problematic window by typing the
following in the relax root directory:

$ grep -r "Wiz_window(" gui/

If the height of 750 fixes the problem for you, I'll change the values
in the code.

Cheers,

Edward




On 30 March 2015 at 22:10, Lora Picton  wrote:
> Hi,
>
> I have relax running on my Ubuntu 12.04 laptop, and am running into a problem 
> with the GUI. When trying to set up spin systems, the spin loading page is 
> unable to be resized, and the buttons at the bottom are not visible, and thus 
> not clickable.
>
> I have tried playing with the resolution and screen sizes on my display, but 
> this did not solve the problem.
>
> Is there a way to make this window either a smaller, fixed size? Alternately, 
> is there a way to add the ability to resize the window?
>
> Thank you so much for your time and attention.
>
> Sincerely,
> Lora Picton
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
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Re: Issue with Pymol/CCPN menus after Relax install

[Edward d'Auvergne]

Hi Lisa,

Welcome to the relax mailing lists!  I think Jack might be able to
answer this better, as he appears to be in charge of these packages at
MacPorts:

https://www.macports.org/ports.php?by=name&substr=relax
https://www.macports.org/ports.php?by=name&substr=pymol
https://www.macports.org/ports.php?by=name&substr=CCPN

When you installed relax for the first time from MacPorts, was there
any other software installed at around the same time?  Especially
non-MacPorts libraries.  For installing relax the second time, did you
use the DMG file at http://www.nmr-relax.com/download.html#Mac_OS_X ?
If so, this is fully independent and shouldn't touch any parts of the
system - all dependencies are built into it.  The problems you see
cannot be due to relax itself, but maybe you could try uninstalling
the MacPorts versions of relax, PyMOL, CCPN and importantly all their
dependencies (py27-numpy py27-scipy py27-wxpython-3.0 pymol python27
scons for relax) and then try to reinstall PyMOL and CCPN.  Maybe it
is the dependencies that are the issue.  Maybe py27-wxpython-3.0
clashes with py27-tkinter, though that is extremely unlikely.  If it
is a tk problem, which I have seen before, then the entire PyMOL tk
window will refuse to start and you'll only have the OpenGL window and
an error message about the tk problem.  It is a very strange problem,
and maybe Jack has better insight as to what is happening.

Regards,

Edward



On 19 March 2015 at 17:44, Lisa Warner  wrote:
> Hi All,
>
> I'm not sure if this is a forum topic or not. Recently all of the menu
> graphics for pymol and ccpn analysis stopped working shortly after I
> installed Relax, which is why I'm posting this. Initially, I installed the
> Macports version of Relax, but then noticed that it wasn't as up-to-date as
> the current distribution on the Stand-Alone distribution on the Relax
> website, so I installed that. It was a short time after that I noticed that
> pymol/analysis menus were not working anymore. The problem could be
> anything at this point, maybe not Relax related at all. I'm just trying to
> figure things out. I think this is a tk-related issue. (I have already
> tried to reinstall with the -no_tkinter suggestion).
>
> My question is this:
>
> Do the python packages that go with the stand-alone Relax get put into or
> overwrite the system files? /usr/bin/?
>
> Even if they do, it shouldn't matter because all of my dependencies for
> Pymol/CCPN should be sourcing the macports install dir /opt/local/bin...
>
> I've uninstalled all Relax and all softwares installed with Macports and
> reinstalled only pymol and it's dependencies to try to tease out the
> problem. But even after removing everything and a fresh install of Pymol, I
> still have the same problem.
>
> I realize this may not even be a problem from Relax, but if you have any
> advice, I'd greatly appreciate it.
>
> Thanks --
> Lisa
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Re: Help with setting up relax files

[Edward d'Auvergne]

Hi Sam,

I've noticed that you are not signed up for the relax-announce mailing
list (https://mail.gna.org/listinfo/relax-announce/).  This list only
receives 6-10 messages per year.  So you probably missed the release
of relax 3.3.7 (http://wiki.nmr-relax.com/Relax_3.3.7).  This version
has the fix for handling your CSV file of peak intensities.

Regards,

Edward


On 27 February 2015 at 08:26, Edward d'Auvergne  wrote:
> Hi Sam,
>
> For relax, you simply input the peak lists.  Using the
> spectrum.read_intensities user function
> (http://www.nmr-relax.com/manual/spectrum_read_intensities.html), you
> can load in peak intensities - either height or volumes - from many
> different spectral software programs.  This includes Sparky, XEasy,
> NMRView, NMRPipe seriesTab, and a generic column formatted text file
> (the Bruker Dynamics Centre format is also supported).  relax is
> designed so that users never have to perform format conversions to
> input or output data.  If a format conversion is necessary, I would
> insist on a new support request being created and an example data file
> attached to it.  Then the support for the format can be quickly added
> to relax (by first implementing system tests).
>
> The problem with conversions is the chance of data loss or a mistake
> being made.  But the conversions in relax are all extensively and
> repeatedly checked via the comprehensive test suite, so that you can
> be sure that no mistakes are made:
>
> $ relax --test-suite --time
>
> But just with all other analysis software, you should always be on the
> look out for problems, as all software contains bugs.  So software can
> be treated as a black box, but always be vigilant and sceptical of all
> results.  Oh, thanks to advances implemented by Troels, you can now
> simultaneously load all peak lists with one spectrum.read_intensities
> user function call.  This is especially useful if you are using the
> GUI.
>
> Regards,
>
> Edward
>
>
>
>
> On 26 February 2015 at 23:58, Sze Chan  wrote:
>>
>> Hello,
>>
>> Currently, I'm collecting more NMR data so I haven't had much time to 
>> analyze the data.
>>
>> Usually, I extract the raw peak heights at each CPMG Hz for each residue 
>> (assignments saved in my ccpnmr project) so I don't have a peaklist for my 
>> CPMG data. The same is done for my fast time scale dynamics (T1/T2/NOE).
>>
>> So I was wondering if there was a way to set up the files in a tabular 
>> format by hand? (an example of such a table would be very helpful). I was 
>> hoping if there was some way to fit my dispersion data just on a per residue 
>> basis, similar to how another NMR program, NESSY, takes in data.
>>
>> Thank you for your time and patience, as an undergrad a lot of the 
>> information and navigation is quite overwhelming so its great to have some 
>> help!
>>
>> Regards,
>> Sam
>> 
>> From: edward.dauver...@gmail.com  on behalf of 
>> Edward d'Auvergne 
>> Sent: Thursday, February 26, 2015 12:32 PM
>> To: Troels Emtekær Linnet
>> Cc: Sze Chan; relax-users@gna.org
>> Subject: Re: Help with setting up relax files
>>
>> Hi Sam,
>>
>> I was wondering if you still had problems with the loading of peak
>> heights for relaxation dispersion in relax?  It should be pretty
>> flexible and handle most formats you throw at relax.  If you have a
>> peak list format that is not supported, it would be appreciated if you
>> could create a support request (https://gna.org/support/?group=relax,
>> https://gna.org/support/?func=additem&group=relax).  If you attach a
>> truncated peak list to the request, slightly randomised if you would
>> like to keep the data private, then that file could be used to quickly
>> implement support for the format.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>>
>> On 15 February 2015 at 10:58, Troels Emtekær Linnet
>>  wrote:
>>> Hi Sam.
>>>
>>>
>>>
>>> Try to have a look on the wiki:
>>> http://wiki.nmr-relax.com/Category:Tutorials
>>>
>>> http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved
>>>
>>> Maybe you can figure out something.
>>>
>>> If you need more help.
>>>
>>> Make a suppert request
>>> https://gna.org/support/?group=relax
>>>
>>> Upload an example peak list for each CPMG frq.
>>> Make a file, listing filename for peaklist and corresponding CPMG frq.
&g

Re: Help with setting up relax files

[Edward d'Auvergne]

Hi Sam,

For relax, you simply input the peak lists.  Using the
spectrum.read_intensities user function
(http://www.nmr-relax.com/manual/spectrum_read_intensities.html), you
can load in peak intensities - either height or volumes - from many
different spectral software programs.  This includes Sparky, XEasy,
NMRView, NMRPipe seriesTab, and a generic column formatted text file
(the Bruker Dynamics Centre format is also supported).  relax is
designed so that users never have to perform format conversions to
input or output data.  If a format conversion is necessary, I would
insist on a new support request being created and an example data file
attached to it.  Then the support for the format can be quickly added
to relax (by first implementing system tests).

The problem with conversions is the chance of data loss or a mistake
being made.  But the conversions in relax are all extensively and
repeatedly checked via the comprehensive test suite, so that you can
be sure that no mistakes are made:

$ relax --test-suite --time

But just with all other analysis software, you should always be on the
look out for problems, as all software contains bugs.  So software can
be treated as a black box, but always be vigilant and sceptical of all
results.  Oh, thanks to advances implemented by Troels, you can now
simultaneously load all peak lists with one spectrum.read_intensities
user function call.  This is especially useful if you are using the
GUI.

Regards,

Edward




On 26 February 2015 at 23:58, Sze Chan  wrote:
>
> Hello,
>
> Currently, I'm collecting more NMR data so I haven't had much time to analyze 
> the data.
>
> Usually, I extract the raw peak heights at each CPMG Hz for each residue 
> (assignments saved in my ccpnmr project) so I don't have a peaklist for my 
> CPMG data. The same is done for my fast time scale dynamics (T1/T2/NOE).
>
> So I was wondering if there was a way to set up the files in a tabular format 
> by hand? (an example of such a table would be very helpful). I was hoping if 
> there was some way to fit my dispersion data just on a per residue basis, 
> similar to how another NMR program, NESSY, takes in data.
>
> Thank you for your time and patience, as an undergrad a lot of the 
> information and navigation is quite overwhelming so its great to have some 
> help!
>
> Regards,
> Sam
> ________
> From: edward.dauver...@gmail.com  on behalf of 
> Edward d'Auvergne 
> Sent: Thursday, February 26, 2015 12:32 PM
> To: Troels Emtekær Linnet
> Cc: Sze Chan; relax-users@gna.org
> Subject: Re: Help with setting up relax files
>
> Hi Sam,
>
> I was wondering if you still had problems with the loading of peak
> heights for relaxation dispersion in relax?  It should be pretty
> flexible and handle most formats you throw at relax.  If you have a
> peak list format that is not supported, it would be appreciated if you
> could create a support request (https://gna.org/support/?group=relax,
> https://gna.org/support/?func=additem&group=relax).  If you attach a
> truncated peak list to the request, slightly randomised if you would
> like to keep the data private, then that file could be used to quickly
> implement support for the format.
>
> Cheers,
>
> Edward
>
>
>
>
> On 15 February 2015 at 10:58, Troels Emtekær Linnet
>  wrote:
>> Hi Sam.
>>
>>
>>
>> Try to have a look on the wiki:
>> http://wiki.nmr-relax.com/Category:Tutorials
>>
>> http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved
>>
>> Maybe you can figure out something.
>>
>> If you need more help.
>>
>> Make a suppert request
>> https://gna.org/support/?group=relax
>>
>> Upload an example peak list for each CPMG frq.
>> Make a file, listing filename for peaklist and corresponding CPMG frq.
>>
>> You need to determine the error of your experiments.
>> If you have peak heights which are replicate/triplicate, then this is fine.
>> Or else you need to measure RMSD of the noise in the spectrum.
>>
>> What is also:
>> Relaxation dispersion CPMG constant time delay T (in s).
>> The NMR field strength of the spectrum. (750 MHz ?)
>>
>> Best
>> Troels
>>
>>
>> 2015-02-15 1:09 GMT+01:00 Sze Chan :
>>
>>> Hello all,
>>>
>>>
>>> I am an undergrad that is new to the field of NMR and I was hoping to get
>>> some basic help in setting up my data for analysis.
>>>
>>>
>>> For my CPMG relaxation dispersion experiments, I usually process my data
>>> through NMR pipe and then extract the peak height

Re: Help with setting up relax files

[Edward d'Auvergne]

Hi Sam,

I was wondering if you still had problems with the loading of peak
heights for relaxation dispersion in relax?  It should be pretty
flexible and handle most formats you throw at relax.  If you have a
peak list format that is not supported, it would be appreciated if you
could create a support request (https://gna.org/support/?group=relax,
https://gna.org/support/?func=additem&group=relax).  If you attach a
truncated peak list to the request, slightly randomised if you would
like to keep the data private, then that file could be used to quickly
implement support for the format.

Cheers,

Edward




On 15 February 2015 at 10:58, Troels Emtekær Linnet
 wrote:
> Hi Sam.
>
>
>
> Try to have a look on the wiki:
> http://wiki.nmr-relax.com/Category:Tutorials
>
> http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved
>
> Maybe you can figure out something.
>
> If you need more help.
>
> Make a suppert request
> https://gna.org/support/?group=relax
>
> Upload an example peak list for each CPMG frq.
> Make a file, listing filename for peaklist and corresponding CPMG frq.
>
> You need to determine the error of your experiments.
> If you have peak heights which are replicate/triplicate, then this is fine.
> Or else you need to measure RMSD of the noise in the spectrum.
>
> What is also:
> Relaxation dispersion CPMG constant time delay T (in s).
> The NMR field strength of the spectrum. (750 MHz ?)
>
> Best
> Troels
>
>
> 2015-02-15 1:09 GMT+01:00 Sze Chan :
>
>> Hello all,
>>
>>
>> I am an undergrad that is new to the field of NMR and I was hoping to get
>> some basic help in setting up my data for analysis.
>>
>>
>> For my CPMG relaxation dispersion experiments, I usually process my data
>> through NMR pipe and then extract the peak heights through ccpnmr with each
>> plane as the CPMG frequency. In the end for each residue, I get the peak
>> height at various CPMG frequencies.
>>
>>
>> However, I'm not sure how to format my table or know what software I can
>> use to format my data so that I can input it into relax. If anyone has any
>> help, I'd greatly appreciate it since I'm very new to the field and all the
>> analysis that comes with it.
>>
>>
>> Regards,
>>
>> Sam
>>
>>
>> Department of Biochemistry - University of Toronto
>> ___
>> relax (http://www.nmr-relax.com)
>>
>> This is the relax-users mailing list
>> relax-users@gna.org
>>
>> To unsubscribe from this list, get a password
>> reminder, or change your subscription options,
>> visit the list information page at
>> https://mail.gna.org/listinfo/relax-users
>>
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users

___
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relax-users@gna.org

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Re: If I can run modelfree analysis using relaxation data from only single magnetic field?

[Edward d'Auvergne]

Hi Danyun,

Welcome to the relax mailing lists!  Hopefully the wiki link that
Troels sent you will be sufficient.  Note that there is a huge amount
of information in the links to previous discussion threads at
http://wiki.nmr-relax.com/Model-free_analysis_single_field#The_Question
which may answer many other questions you might have.  I have also
added this email thread
(http://thread.gmane.org/gmane.science.nmr.relax.user/1800) to the
wiki page for future reference.

Regards,

Edward


On 28 January 2015 at 09:47, Troels Emtekær Linnet
 wrote:
> Hi Danyun Zeng.
>
> Try have a look on this wiki page:
> http://wiki.nmr-relax.com/Model-free_analysis_single_field
>
> Best
> Troels
>
> 2015-01-28 1:13 GMT+01:00 Danyun Zeng :
>
>> Hi, all,
>>
>> I'm new to relax. I want to use it for modelfree analysis recently and I
>> only have a set of relaxation data from 500MHz NMR spectrometer.
>> May I ask if I can run modelfree analysis using relaxation data from only
>> single magnetic field? All the sample scripts in relax's manual requires
>> data at least from 2 fields. I haven't find a way to do that.
>> I heard ModelFree4 can do it. But that software is kind of old, and I have
>> to separately calculate r1 r2 noe. That's why I still want to try relax
>> first. If anyone can teach me, I really appreciate!
>>
>> Best regards,
>> Danyun
>>
>> Postdoctoral fellow
>>
>> Department of Biochemistry & Biophysics
>> Texas A&M University
>> ___
>> relax (http://www.nmr-relax.com)
>>
>> This is the relax-users mailing list
>> relax-users@gna.org
>>
>> To unsubscribe from this list, get a password
>> reminder, or change your subscription options,
>> visit the list information page at
>> https://mail.gna.org/listinfo/relax-users
>>
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users

___
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relax-users@gna.org

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reminder, or change your subscription options,
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Re: Error calculation of individual parameter "dw" from MC

[Edward d'Auvergne]

Hi,

Ok, I can now see that the lines

if not param_name in ['r2eff', 'i0']:
si = 0

could be a problem.  The 'not' part should probably not be there!
This code was introduced at:

http://article.gmane.org/gmane.science.nmr.relax.scm/17945

Once this important bug is fixed (https://gna.org/bugs/?23186), and
the relax test suite still passes, I'll make a new relax 3.3.5 release
(http://wiki.nmr-relax.com/Category:Release_Notes).

Cheers,

Edward



On 14 January 2015 at 14:05, Edward d'Auvergne  wrote:
> Hi Troels,
>
> I guess this is for a clustered analysis?  Would you be able to create
> a system test which demonstrates this problem?  Two spins with two or
> three MC simulations would be sufficient.  The code you've identified
> in the specific_analyses.relax_disp.api.sim_return_param() function
> should work, as the spin index si comes from the
> param_index_to_param_info() function.  If anything, it is that
> function in the specific_analyses/relax_disp/parameters.py file which
> does not correctly find the spin index, and that function uses the
> relaxation dispersion loop_parameters() function to identify the
> parameter.  From the code, I don't see any problems:
>
> http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.api-pysrc.html#Relax_disp.sim_return_param
> http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#param_index_to_param_info
> http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#loop_parameters
>
> Cheers,
>
> Edward
>
> On 14 January 2015 at 13:42, Troels Emtekær Linnet  wrote:
>> If I do it for the first spin:
>>
>> cdp.mol[0].res[0].spin[0].dw_sim
>>
>> import numpy as np
>>
>> a = np.array([0.9451997476845593, 0.8054522239552819, 0.9277366066500237,
>> 0.9625036075584432, 0.8802059033496906, 0.9972921559805459,
>> 0.8743682211305104, 0.9500671171775412, 0.9155241775057494,
>> 0.9468124355863968, 0.96417019553941, 1.0170148731646576,
>> 0.808583141857603, 0.9101215951359578, 0.950865223270674,
>> 1.0307772448494004, 0.8993891518585049, 0.9139606433668193,
>> 0.956733004106492, 0.8978513006468936, 0.9453834676054009,
>> 0.910827776695774, 0.8808826708447804, 0.9260230255021042,
>> 0.9502172231153962, 0.86537440977864, 0.8859323973019857,
>> 0.8893764312486083, 0.9731605295027338, 1.0041329485057724,
>> 0.9484007034626689, 0.8562407086263037, 0.8949760705986323,
>> 0.9494159177232087, 0.9536607612740096, 0.981423499818791,
>> 0.8795248912995862, 0.9703162419092174, 0.9498731423252795,
>> 0.8766210928540752, 0.8716559260505473, 0.9697324548237327,
>> 0.8330252500434963, 0.9463453433710509, 0.8936136907056889,
>> 0.9393334443985975, 0.9310091998291463, 0.9409086436225335,
>> 0.9194230869394555, 0.9150169906828444, 0.937755163159723,
>> 0.821586577578577, 0.8844807208799657, 0.9509710398156324,
>> 0.9244476893902771, 0.8912100177428832, 0.8667907082691229,
>> 0.8523582565296183, 0.911207452505568, 0.8546152190640066,
>> 0.8797463442344267, 0.932394336758319, 0.965515026672257,
>> 0.8967984708313228, 0.9562847792473697, 0.9662836189055034,
>> 0.9187032714923455, 0.9552991998159039, 0.8721372679559742,
>> 0.951677098087865, 0.970701220083394, 0.880277858875798,
>> 0.8868837879487532, 0.8289936757848054, 0.8452643978000389,
>> 0.8608520989786752, 0.9408859834978103, 0.9477671884481794,
>> 0.9355182739828974, 0.9058402170229929, 0.888170996310456,
>> 0.8872799805467638, 0.872024994152445, 0.8802787599729809,
>> 0.9527566512472332, 0.8864763874519584, 0.8436371510886024,
>> 0.9828573401629994, 0.9771419297773668, 0.906019424908,
>> 0.9707157553507724, 0.879689193482642, 0.9436375392843368,
>> 0.9927180210208233, 0.9267041637380232, 0.9412299434835303,
>> 0.926346676233505, 0.8774254634406635, 0.8826805167518188,
>> 0.8865687070701256, 0.9512379465525047, 0.9641813779931143,
>> 0.953277273069755, 1.0047488071722177, 0.8521615788684946,
>> 0.8680916457728691, 0.9340561986882852, 0.9477037339014749,
>> 0.9469454099421577, 0.9005897924118794, 0.8803998440278067,
>> 0.9024692253200567, 0.909122984887152, 0.8399468552579564,
>> 0.9571308078096232, 0.9683939646310176, 0.9419649402214831,
>> 0.9613040120941247, 0.9781781986426726, 0.9805816556476108,
>> 0.94937687356695, 0.960693374108915, 0.9530824549428941,
>> 0.8843910508664925, 0.8945735422767003, 0.9049315573495563,
>> 0.8802084472126279, 0.8328713211676385, 0.9406572364992218,
>> 0.910325290850831, 0.9318781551216802, 0.8934350965988851,
>> 0.8353799932488288, 0.951313819820305, 0.855414485205892,
>> 0.909

Re: Error calculation of individual parameter "dw" from MC

[Edward d'Auvergne]

Hi Troels,

I guess this is for a clustered analysis?  Would you be able to create
a system test which demonstrates this problem?  Two spins with two or
three MC simulations would be sufficient.  The code you've identified
in the specific_analyses.relax_disp.api.sim_return_param() function
should work, as the spin index si comes from the
param_index_to_param_info() function.  If anything, it is that
function in the specific_analyses/relax_disp/parameters.py file which
does not correctly find the spin index, and that function uses the
relaxation dispersion loop_parameters() function to identify the
parameter.  From the code, I don't see any problems:

http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.api-pysrc.html#Relax_disp.sim_return_param
http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#param_index_to_param_info
http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#loop_parameters

Cheers,

Edward

On 14 January 2015 at 13:42, Troels Emtekær Linnet  wrote:
> If I do it for the first spin:
>
> cdp.mol[0].res[0].spin[0].dw_sim
>
> import numpy as np
>
> a = np.array([0.9451997476845593, 0.8054522239552819, 0.9277366066500237,
> 0.9625036075584432, 0.8802059033496906, 0.9972921559805459,
> 0.8743682211305104, 0.9500671171775412, 0.9155241775057494,
> 0.9468124355863968, 0.96417019553941, 1.0170148731646576,
> 0.808583141857603, 0.9101215951359578, 0.950865223270674,
> 1.0307772448494004, 0.8993891518585049, 0.9139606433668193,
> 0.956733004106492, 0.8978513006468936, 0.9453834676054009,
> 0.910827776695774, 0.8808826708447804, 0.9260230255021042,
> 0.9502172231153962, 0.86537440977864, 0.8859323973019857,
> 0.8893764312486083, 0.9731605295027338, 1.0041329485057724,
> 0.9484007034626689, 0.8562407086263037, 0.8949760705986323,
> 0.9494159177232087, 0.9536607612740096, 0.981423499818791,
> 0.8795248912995862, 0.9703162419092174, 0.9498731423252795,
> 0.8766210928540752, 0.8716559260505473, 0.9697324548237327,
> 0.8330252500434963, 0.9463453433710509, 0.8936136907056889,
> 0.9393334443985975, 0.9310091998291463, 0.9409086436225335,
> 0.9194230869394555, 0.9150169906828444, 0.937755163159723,
> 0.821586577578577, 0.8844807208799657, 0.9509710398156324,
> 0.9244476893902771, 0.8912100177428832, 0.8667907082691229,
> 0.8523582565296183, 0.911207452505568, 0.8546152190640066,
> 0.8797463442344267, 0.932394336758319, 0.965515026672257,
> 0.8967984708313228, 0.9562847792473697, 0.9662836189055034,
> 0.9187032714923455, 0.9552991998159039, 0.8721372679559742,
> 0.951677098087865, 0.970701220083394, 0.880277858875798,
> 0.8868837879487532, 0.8289936757848054, 0.8452643978000389,
> 0.8608520989786752, 0.9408859834978103, 0.9477671884481794,
> 0.9355182739828974, 0.9058402170229929, 0.888170996310456,
> 0.8872799805467638, 0.872024994152445, 0.8802787599729809,
> 0.9527566512472332, 0.8864763874519584, 0.8436371510886024,
> 0.9828573401629994, 0.9771419297773668, 0.906019424908,
> 0.9707157553507724, 0.879689193482642, 0.9436375392843368,
> 0.9927180210208233, 0.9267041637380232, 0.9412299434835303,
> 0.926346676233505, 0.8774254634406635, 0.8826805167518188,
> 0.8865687070701256, 0.9512379465525047, 0.9641813779931143,
> 0.953277273069755, 1.0047488071722177, 0.8521615788684946,
> 0.8680916457728691, 0.9340561986882852, 0.9477037339014749,
> 0.9469454099421577, 0.9005897924118794, 0.8803998440278067,
> 0.9024692253200567, 0.909122984887152, 0.8399468552579564,
> 0.9571308078096232, 0.9683939646310176, 0.9419649402214831,
> 0.9613040120941247, 0.9781781986426726, 0.9805816556476108,
> 0.94937687356695, 0.960693374108915, 0.9530824549428941,
> 0.8843910508664925, 0.8945735422767003, 0.9049315573495563,
> 0.8802084472126279, 0.8328713211676385, 0.9406572364992218,
> 0.910325290850831, 0.9318781551216802, 0.8934350965988851,
> 0.8353799932488288, 0.951313819820305, 0.855414485205892,
> 0.909767822028357, 0.8924203614902587, 0.9408505916987862,
> 0.8751269857340623, 0.938822046542, 0.9499696867836579,
> 0.9605708328530759, 0.9054195520491586, 0.8859714100727238,
> 0.9305256454920723, 0.937758620326129, 0.9320519159136575,
> 0.9656009544636446, 0.9584255887448183, 0.8738507316066699,
> 0.9661737748832995, 0.8717799481773607, 0.959731591608098,
> 0.9640387155993229, 0.8600096309525227, 0.8762991916520275,
> 0.9329290121054334, 0.838440295115923, 0.8399242891708862,
> 0.8145405034437483, 0.961537851810333, 0.9430802765990043,
> 0.9358230046912992, 0.9359556594347389, 0.9553690216306725,
> 0.9943161816393639, 0.9823102347443102, 0.9586429773877578,
> 0.9599901351410914, 0.9229179343561751, 0.9481274587922217,
> 0.8970870418193109, 0.9940991138386224, 0.8321641241392229,
> 0.820820360597734, 0.9239612738883967, 0.8028677971498746,
> 0.9470524563800362, 0.8770948453727446, 0.8786234926518741,
> 0.9500563596927654, 0.9425646627827216, 0.9813509472882151,
> 0.8963925974037248, 0.9665748645186323, 0.9481002238259164,
> 0.9762925493355714, 0.944890

Re: error on the diffusion tensor parameters

[Edward d'Auvergne]

Hi Vineet,

After an analysis, anything is possible using the relax user
functions.  That includes performing Monte Carlo simulations on any
model you wish.  Have a look at some of the sample scripts for the
sequence of user functions required.

Regards,

Edward



On 18 December 2014 at 16:33, Panwalkar, Vineet
 wrote:
> Hello Edward,
>
> Thanks for the reply. I am trying to get hold of all the missing modules. 
> Once they are all at one place, I will put it into relax with his permission.
>
> I had another small query. I was wondering if there was a possibility to 
> extract errors on the model free parameters within all the four diffusion 
> tensor models. I mean, normally, the MC simulations are performed once a 
> particular diffusion tensor is selected using the AIC. Is there a way to do 
> the this on rest of the tensor models as well, either before the AIC 
> selection or after it separately?
>
> Regards,
>
> Vineet
> 
> An: Panwalkar, Vineet
> Cc: relax-users@gna.org
> Betreff: Re: error on the diffusion tensor parameters
>
> Hi Vineet,
>
> From the error message, the my_relax module is clearly a special
> Python or relax module written by your former college.  It is not part
> of relax, so I can't help you much.  You might be able to find it on
> your system by typing:
>
> $ locate my_relax.py
> $ locate tensor_mc.py
>
> The missing external module will have one of these names.  If it is
> tensor_mc.py, then this will be in the directory "my_relax/".  All the
> contents of that directory is then called a Python package, and you
> will need all of it.  I hope this information helps.  It is a pity
> your former college did not contribute it to relax so that I can help
> you more.
>
> Regards,
>
> Edward
>
>
> On 18 December 2014 at 15:36, Panwalkar, Vineet
>  wrote:
>> Dear Edward,
>>
>> Following is the error,
>>
>> Traceback (most recent call last):
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py", 
>> line 494, in run
>> self.callback.init_master(self)
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py", 
>> line 318, in default_init_master
>> self.master.run()
>>   File "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py", line 
>> 199, in run
>> self.interpreter.run(self.script_file)
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py",
>>  line 279, in run
>> return run_script(intro=self.__intro_string, local=locals(), 
>> script_file=script_file, show_script=self.__show_script, 
>> raise_relax_error=self.__raise_relax_error)
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py",
>>  line 585, in run_script
>> return console.interact(intro, local, script_file, 
>> show_script=show_script, raise_relax_error=raise_relax_error)
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py",
>>  line 484, in interact_script
>> exec_script(script_file, local)
>>   File 
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py",
>>  line 363, in exec_script
>> runpy.run_module(module, globals)
>>   File "/opt/scisoft64/usr/lib/python2.7/runpy.py", line 180, in run_module
>> fname, loader, pkg_name)
>>   File "/opt/scisoft64/usr/lib/python2.7/runpy.py", line 72, in _run_code
>> exec code in run_globals
>>   File 
>> "/home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py",
>>  line 11, in 
>> from my_relax.tensor_mc import Main, print_fancy, Out_tensor
>> ImportError: No module named my_relax.tensor_mc
>>
>> I am checking with my former labmate who wrote the script regarding the 
>> module as well.
>>
>> I also had a question regarding possibility of performing Monte Carlo 
>> simulations to get errors on the model free parameters within all the four 
>> diffusion tensor models. I mean, normally, the MC simulations are performed 
>> once a particular diffusion tensor is selected using the AIC. Is there a way 
>> to do the simulations on rest of the tensor models as well?
>>
>> Cheers,
>>
>> Vineet
>> 
>>
>> Hi Vineet,
>>
>> Could you copy and paste the entire error?  That would significantly
>> help working out what is happening, as it will indicate where the
>> error is happening.  But if you search for the text "my_relax" or file
>> "my_relax.py", you will see that this has never existed in any version
>> of relax, from 2001 until now.
>>
>> Regards,
>>
>> Edward
>>
>>  ___
>>
>> On 18 December 2014 at 15:09, Panwalkar, Vineet
>>> Hi all,
>>>
>>> I have a script to calculate errors on the diffusion tensor parameters, 
>>> written by one of my former colleagues. It works well with relax v 3.2.3 
>>> however, in the version 3.3.3, it doesn't work and gives an error message 
>>>

Re: error on the diffusion tensor parameters

[Edward d'Auvergne]

Hi Vineet,

>From the error message, the my_relax module is clearly a special
Python or relax module written by your former college.  It is not part
of relax, so I can't help you much.  You might be able to find it on
your system by typing:

$ locate my_relax.py
$ locate tensor_mc.py

The missing external module will have one of these names.  If it is
tensor_mc.py, then this will be in the directory "my_relax/".  All the
contents of that directory is then called a Python package, and you
will need all of it.  I hope this information helps.  It is a pity
your former college did not contribute it to relax so that I can help
you more.

Regards,

Edward


On 18 December 2014 at 15:36, Panwalkar, Vineet
 wrote:
> Dear Edward,
>
> Following is the error,
>
> Traceback (most recent call last):
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py", 
> line 494, in run
> self.callback.init_master(self)
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py", 
> line 318, in default_init_master
> self.master.run()
>   File "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py", line 
> 199, in run
> self.interpreter.run(self.script_file)
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py", 
> line 279, in run
> return run_script(intro=self.__intro_string, local=locals(), 
> script_file=script_file, show_script=self.__show_script, 
> raise_relax_error=self.__raise_relax_error)
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py", 
> line 585, in run_script
> return console.interact(intro, local, script_file, 
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py", 
> line 484, in interact_script
> exec_script(script_file, local)
>   File 
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py", 
> line 363, in exec_script
> runpy.run_module(module, globals)
>   File "/opt/scisoft64/usr/lib/python2.7/runpy.py", line 180, in run_module
> fname, loader, pkg_name)
>   File "/opt/scisoft64/usr/lib/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
>   File 
> "/home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py",
>  line 11, in 
> from my_relax.tensor_mc import Main, print_fancy, Out_tensor
> ImportError: No module named my_relax.tensor_mc
>
> I am checking with my former labmate who wrote the script regarding the 
> module as well.
>
> I also had a question regarding possibility of performing Monte Carlo 
> simulations to get errors on the model free parameters within all the four 
> diffusion tensor models. I mean, normally, the MC simulations are performed 
> once a particular diffusion tensor is selected using the AIC. Is there a way 
> to do the simulations on rest of the tensor models as well?
>
> Cheers,
>
> Vineet
> 
>
> Hi Vineet,
>
> Could you copy and paste the entire error?  That would significantly
> help working out what is happening, as it will indicate where the
> error is happening.  But if you search for the text "my_relax" or file
> "my_relax.py", you will see that this has never existed in any version
> of relax, from 2001 until now.
>
> Regards,
>
> Edward
>
>  ___
>
> On 18 December 2014 at 15:09, Panwalkar, Vineet
>> Hi all,
>>
>> I have a script to calculate errors on the diffusion tensor parameters, 
>> written by one of my former colleagues. It works well with relax v 3.2.3 
>> however, in the version 3.3.3, it doesn't work and gives an error message 
>> saying "ImportError: No module named my_relax.tensor_mc".
>> I was wondering if the module has been renamed/replaced to something else or 
>> is this something entirely different.
>>
>> Thanks,
>>
>> Vineet
>> ___
>> relax (http://www.nmr-relax.com)
>>
>> This is the relax-users mailing list
>> relax-users@gna.org
>>
>> To unsubscribe from this list, get a password
>> reminder, or change your subscription options,
>> visit the list information page at
>> https://mail.gna.org/listinfo/relax-users
>
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> --

Re: error on the diffusion tensor parameters

[Edward d'Auvergne]

Hi Vineet,

Could you copy and paste the entire error?  That would significantly
help working out what is happening, as it will indicate where the
error is happening.  But if you search for the text "my_relax" or file
"my_relax.py", you will see that this has never existed in any version
of relax, from 2001 until now.

Regards,

Edward



On 18 December 2014 at 15:09, Panwalkar, Vineet
 wrote:
> Hi all,
>
> I have a script to calculate errors on the diffusion tensor parameters, 
> written by one of my former colleagues. It works well with relax v 3.2.3 
> however, in the version 3.3.3, it doesn't work and gives an error message 
> saying "ImportError: No module named my_relax.tensor_mc".
> I was wondering if the module has been renamed/replaced to something else or 
> is this something entirely different.
>
> Thanks,
>
> Vineet
>
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
>
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users

___
relax (http://www.nmr-relax.com)

This is the relax-users mailing list
relax-users@gna.org

To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users

Re: What happens if I try to do MF analysis only having 800mHz data?

[Edward d'Auvergne]

Hi Sean,

Welcome to the relax mailing lists!  I'll start by explaining how
relax can handle your single field strength data.  Firstly, I need to
point out that relax can do everything Modelfree4 does and it can
replicate the results of Modelfree4 exactly (well, almost, as real
constraint algorithms are used in relax and that used by Modelfree4
will never be added to relax).  I used this replication of Modelfree4
and Dasha behaviour as the basis for my 2008 papers
(http://dx.doi.org/10.1007/s10858-007-9214-2,
http://dx.doi.org/10.1007/s10858-007-9213-3), for understanding why
these two softwares produce sometimes quite different results.  I
don't think this was mentioned in the papers or supplement as is it so
basic in relax to do - you simply pick the same optimisation algorithm
as the other software and decrease the optimisation precision and
maximum number of optimisation iterations to match (see table 1 of the
first paper for these).

So, to perform your analysis, you need to note the difference between
the theory and optimising the model-free models verses a full analysis
protocol.  These are very different and it confuses a lot of people.
The former is fast and only takes minutes to an hour.  The later is
super-iterative and much slower, taking a day to 1-2 weeks.   There is
a lot of software out there that implements the former (Modelfree4,
Dasha, Tensor2, DYNAMICS), and then you are expected to manually take
the steps required for fulfilling the full protocol yourself (some
people don't know this and end up publishing very questionable
dynamics).  So what are the protocols?  The first full protocol was
published in the Mandel et al, 1995 paper:

http://www.nmr-relax.com/manual/The_methodology_of_Mandel_et_al_1995.html

When implemented correctly, this takes an incredible amount of time as
expensive Monte Carlo simulations are performed at each step and each
model to obtain the chi2 and F-test statistics.  As I published in my
2003 model selection paper
(http://dx.doi.org/10.1023/A:1021902006114), this should not be used.
This introduces, deliberately I should note, or the original paper
notes, bias towards the simpler models and hence less motion.  Another
major problem is the F-test.  The F-test is useful for comparing
models, but there is fine print the most people don't know about.  The
F-test is only statistically valid when the two models compared are
nested!  This is mentioned in the Numerical Recipes book series, for
example.  As The next protocol I designed based on this one and it
handles single field strength data:

http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html

It is similar in that you need and initial diffusion tensor estimate.
However it replaces the chi-squared, F-tests, and chi-squared value
empirical cut-offs with statistical AIC model selection, introduces
the concept of model elimination
(http://dx.doi.org/10.1007/s10858-006-9007-z), removes the need for
intermediate Monte Carlo simulations, and simplifies the flow of
operation.  The last protocol I'll mention here is the one I devised
to eliminate the problems associated with the initial diffusion tensor
estimate:

http://www.nmr-relax.com/manual/The_new_model_free_optimisation_protocol.html
http://www.nmr-relax.com/manual/Model_free_analysis_in_reverse.html

This is the protocol from my second 2008 paper
(http://dx.doi.org/10.1007/s10858-007-9213-3).  If you are using the
relax model-free auto-analysis (called the dauvergne_protocol, see
http://www.nmr-relax.com/api/3.3/auto_analyses.dauvergne_protocol-module.html)
or the graphical user interface (GUI), you will be using this
protocol.  I have implemented it as a fully automated auto-analysis
which is essentially just a complicated relax script.  Although this
protocol solves all of the earlier problems with model-free analyses
(protocols), it absolutely requires data at two fields.

So, how do you implement the protocol of
http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html for
single field strength data?  I have answered this many times on the
relax mailing lists, and it has been summarised in the following relax
wiki article:

http://wiki.nmr-relax.com/Model-free_analysis_single_field

You will find the links to the discussions there highly informative!
For the protocol described therein, most steps are present as
individual scripts in the sample_scripts/model_free/ directory.  I
have not merged these together into an automated analysis yet, mainly
due to the horrendous artefacts of using single field strength data
that are often interpreted as real dynamics.  The first step is to
obtain the initial diffusion tensor estimate.  There is no script for
this as most people use Tensor2 for this.  Neither Modelfree4 nor
Dasha implement this.  However this is not ideal as there is no clear
mapping of the spherical angles and Euler angles between Tensor2,
Modelfree4, Dasha, DYNAMICS, and relax (due to lack of documentation).
For the rest, I'll let

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Prem,

From the error message, this is within the automated analysis for
relaxation dispersion.  Creating the data pipe 'R2eff - relax_disp
(Mon Nov 17 10:50:08 2014)' can only happen once, as the 'R2eff' model
is only optimised once (there is a loop over all models).  There is
only one thing I can think of, and that is that the analysis was run
with OpenMPI.  However if the "--multi='mpi4py'" part of the full
command:

$ mpirun -np 8 relax --multi='mpi4py'

is missing, as:

$ mpirun -np 8 relax

Then this problem might be encountered.  Could that be what happened?
Another cause could be if the 'R2eff' model is passed into the
dispersion auto-analysis more than once in the model list though, as
you are using the GUI, this is not possible.

Cheers,

Edward




On 18 November 2014 at 22:58, Prem Raj Joseph  wrote:
> Hello Edward,
>
> I tried the GUI version of the setup again for the relaxation dispersion
> (on the test data) and it ran without any error this time. Its possible I
> made some mistake during the setup thr last time.
>
> Thank again for the help
>
> Prem
>
>
>
> On Tue, Nov 18, 2014 at 5:27 AM, Edward d'Auvergne 
> wrote:
>
>> Hi Troels and Prem,
>>
>> Troels, for a suggestion for improving the script in your tutorial,
>> you could use:
>>
>> """
>> from time import asctime, localtime
>>
>> pipe_bundle = "relax_disp (%s)" % asctime(localtime())
>> pipe_name = "origin - %s" % pipe_bundle
>> """
>>
>> This is how the new analysis wizard in relax creates these names
>> (
>> http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display
>> ).
>> This script really saves a lot of time.  But, as it does not replicate
>> the bug, Prem, could you still create the bug report and include all
>> steps required to produce the error you observed?
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 18 November 2014 12:08, Troels Emtekær Linnet 
>> wrote:
>> > Hi Prem.
>> >
>> > I added the tutorial here:
>> >
>> >
>> http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
>> >
>> > I tried to take power of the scripting, to get around the tedious work on
>> > defining the experiment settings for all spectra.
>> >
>> > So this script should take you to the "end point" before staring the
>> > analysis.
>> >
>> > Best
>> > Troels
>> >
>> >
>> >
>> > 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet > >:
>> >
>> >> Dear Prem.
>> >>
>> >> Welcome to the mailing list!
>> >>
>> >> I guess that you mean the manual at:
>> >> http://www.nmr-relax.com/manual/Contents.html
>> >>
>> >> The relaxation dispersion auto-analysis in the GUI
>> >>
>> >>
>> http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
>> >>
>> >> Where the test data is in:
>> >> test_suite/shared_data/dispersion/Hansen
>> >>
>> >> I will write it up here as a script instead.
>> >> This goes a little faster testing.
>> >>
>> >> You can also find more inspiration at the wiki:
>> >> http://wiki.nmr-relax.com
>> >> http://wiki.nmr-relax.com/Category:Tutorials
>> >>
>> >> In terminal
>> >> mkdir -p $HOME/test
>> >> cd $HOME/test
>> >> gedit test.py
>> >>
>> >> Then I build the script onwards.
>> >> I run relax repeatedly, to execute code. Then I write new code in the
>> >> script, and run again.
>> >> relax test.py
>> >>
>> >> When I am satisfied, you can then do like this.
>> >>
>> >> relax -g -t log.txt
>> >> User functions -> Script -> test.py
>> >>
>> >> THEN:
>> >> View -> Data pipe editor -> Right click on pipe -> Associate with a new
>> >> Auto analysis
>> >>
>> >> This should bring you to a window, where all settings have been set.
>> >>
>> >> Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG
>> 2-site
>> >> expanded']
>> >> Grid increements: 11 (For speed-up in test phase)
>> >> Monte-Carlo simulations number: 5 (F

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Troels,

For the tutorial at
http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
, I would suggest also adding that relax can be run using OpenMPI to
speed up the relaxation dispersion analysis.  So that if you have a
machine with 8 cores and OpenMPI and python-mpi4py installed
(http://www.nmr-relax.com/manual/The_multi_processor_framework.html),
you can run relax with 7 slaves by typing:

$ mpirun -n 8 relax --multi='mpi4py' --gui --tee my.log

Regards,

Edward



On 18 November 2014 12:27, Edward d'Auvergne  wrote:
> Hi Troels and Prem,
>
> Troels, for a suggestion for improving the script in your tutorial,
> you could use:
>
> """
> from time import asctime, localtime
>
> pipe_bundle = "relax_disp (%s)" % asctime(localtime())
> pipe_name = "origin - %s" % pipe_bundle
> """
>
> This is how the new analysis wizard in relax creates these names
> (http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display).
> This script really saves a lot of time.  But, as it does not replicate
> the bug, Prem, could you still create the bug report and include all
> steps required to produce the error you observed?
>
> Cheers,
>
> Edward
>
>
>
> On 18 November 2014 12:08, Troels Emtekær Linnet  
> wrote:
>> Hi Prem.
>>
>> I added the tutorial here:
>>
>> http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
>>
>> I tried to take power of the scripting, to get around the tedious work on
>> defining the experiment settings for all spectra.
>>
>> So this script should take you to the "end point" before staring the
>> analysis.
>>
>> Best
>> Troels
>>
>>
>>
>> 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet :
>>
>>> Dear Prem.
>>>
>>> Welcome to the mailing list!
>>>
>>> I guess that you mean the manual at:
>>> http://www.nmr-relax.com/manual/Contents.html
>>>
>>> The relaxation dispersion auto-analysis in the GUI
>>>
>>> http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
>>>
>>> Where the test data is in:
>>> test_suite/shared_data/dispersion/Hansen
>>>
>>> I will write it up here as a script instead.
>>> This goes a little faster testing.
>>>
>>> You can also find more inspiration at the wiki:
>>> http://wiki.nmr-relax.com
>>> http://wiki.nmr-relax.com/Category:Tutorials
>>>
>>> In terminal
>>> mkdir -p $HOME/test
>>> cd $HOME/test
>>> gedit test.py
>>>
>>> Then I build the script onwards.
>>> I run relax repeatedly, to execute code. Then I write new code in the
>>> script, and run again.
>>> relax test.py
>>>
>>> When I am satisfied, you can then do like this.
>>>
>>> relax -g -t log.txt
>>> User functions -> Script -> test.py
>>>
>>> THEN:
>>> View -> Data pipe editor -> Right click on pipe -> Associate with a new
>>> Auto analysis
>>>
>>> This should bring you to a window, where all settings have been set.
>>>
>>> Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site
>>> expanded']
>>> Grid increements: 11 (For speed-up in test phase)
>>> Monte-Carlo simulations number: 5 (For speed up in test phase)
>>>
>>> Then a quick click on spin.isotope function, and GO.
>>>
>>>
>>>
>>> test.py
>>> 
>>> #python modules
>>> import os
>>> import glob
>>>
>>> # relax modules
>>> from lib.io import sort_filenames
>>>
>>> # Set path to data
>>> data =
>>> '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'
>>>
>>> # Create the data pipe.
>>> pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
>>> pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
>>> pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
>>> pipe_type='relax_disp')
>>>
>>> # Create spin to hold data.
>>> sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
>>> res_name_col=2)
>>> deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
>>> spin_id_col=None, mol_name_col=None, 

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Troels and Prem,

Troels, for a suggestion for improving the script in your tutorial,
you could use:

"""
from time import asctime, localtime

pipe_bundle = "relax_disp (%s)" % asctime(localtime())
pipe_name = "origin - %s" % pipe_bundle
"""

This is how the new analysis wizard in relax creates these names
(http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display).
This script really saves a lot of time.  But, as it does not replicate
the bug, Prem, could you still create the bug report and include all
steps required to produce the error you observed?

Cheers,

Edward



On 18 November 2014 12:08, Troels Emtekær Linnet  wrote:
> Hi Prem.
>
> I added the tutorial here:
>
> http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
>
> I tried to take power of the scripting, to get around the tedious work on
> defining the experiment settings for all spectra.
>
> So this script should take you to the "end point" before staring the
> analysis.
>
> Best
> Troels
>
>
>
> 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet :
>
>> Dear Prem.
>>
>> Welcome to the mailing list!
>>
>> I guess that you mean the manual at:
>> http://www.nmr-relax.com/manual/Contents.html
>>
>> The relaxation dispersion auto-analysis in the GUI
>>
>> http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
>>
>> Where the test data is in:
>> test_suite/shared_data/dispersion/Hansen
>>
>> I will write it up here as a script instead.
>> This goes a little faster testing.
>>
>> You can also find more inspiration at the wiki:
>> http://wiki.nmr-relax.com
>> http://wiki.nmr-relax.com/Category:Tutorials
>>
>> In terminal
>> mkdir -p $HOME/test
>> cd $HOME/test
>> gedit test.py
>>
>> Then I build the script onwards.
>> I run relax repeatedly, to execute code. Then I write new code in the
>> script, and run again.
>> relax test.py
>>
>> When I am satisfied, you can then do like this.
>>
>> relax -g -t log.txt
>> User functions -> Script -> test.py
>>
>> THEN:
>> View -> Data pipe editor -> Right click on pipe -> Associate with a new
>> Auto analysis
>>
>> This should bring you to a window, where all settings have been set.
>>
>> Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site
>> expanded']
>> Grid increements: 11 (For speed-up in test phase)
>> Monte-Carlo simulations number: 5 (For speed up in test phase)
>>
>> Then a quick click on spin.isotope function, and GO.
>>
>>
>>
>> test.py
>> 
>> #python modules
>> import os
>> import glob
>>
>> # relax modules
>> from lib.io import sort_filenames
>>
>> # Set path to data
>> data =
>> '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'
>>
>> # Create the data pipe.
>> pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
>> pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
>> pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
>> pipe_type='relax_disp')
>>
>> # Create spin to hold data.
>> sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
>> res_name_col=2)
>> deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
>> spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND',
>> change_all=False)
>> deselect.read(file='unresolved', dir=data+os.sep+'800_MHz',
>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
>> boolean='AND', change_all=False)
>>
>> # Give the spins attributes.
>> spin.isotope(isotope='15N', spin_id='@*', force=True)
>> spin.name(name='N')
>>
>> # Do for 800.
>> ###
>> # Change directory.
>> os.chdir(data + os.sep + '500_MHz')
>>
>> # Get the file list, and sort the file list Alphanumeric.
>> flist500 = glob.glob('*.in_sparky')
>> flist500 = sort_filenames(filenames=flist500)
>>
>> # Make ID
>> ID500 = []
>> for f in flist500: ID500.append("500_"+f.split(".in_sparky")[0])
>>
>> # Then Read
>> spectrum.read_intensities(file=flist500, spectrum_id=ID500)
>>
>> # Repeat for the replicated spectra.
>> flist500rep = glob.glob('*in.bis_sparky')
>> flist500rep = sort_filenames(filenames=flist500rep)
>>
>> # Make ID
>> ID500rep = []
>> for f in flist500rep:
>> ID500rep.append("500_"+f.split(".in.bis_sparky")[0]+'b')
>>
>> # Then Read
>> spectrum.read_intensities(file=flist500rep, spectrum_id=ID500rep)
>>
>> # Then map replicated
>> for b_id in ID500rep:
>> a_id = b_id[:-1]
>> spectrum.replicated(spectrum_ids=[a_id, b_id])
>>
>> # Then check
>> print cdp.replicates
>>
>> # Then repeat for 800.
>> ###
>> # Change directory.
>> os.chdir(data + os.sep + '800_MHz')
>>
>> # Get the file list, and sort the file list Alphanumeric.
>> flist800 = glob.glob('*.in_sparky')
>> flist800 = sort_filenames(filenames=flist800)
>>
>> # Make ID
>> ID800 = []
>> for f in flist800: ID800.append("800_"+f.split(".in_sparky")[0])
>>
>> # Then Read
>> spectrum.read_intensities(file=flist800,

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Prem,

Welcome to the relax mailing lists!  For the problem you are seeing,
could you please create a bug report for this
(https://gna.org/bugs/?func=additem&group=relax)?  Cheers!  It would
be good to know what steps you took to encounter this bug, and where
in the analysis the problem occurred.  The more details you give, the
easier it will be for me to reproduce the problem.  Once a relax
developer can reproduce a bug (via a system test), then a solution
often only takes 5 to 10 minutes to implement.  The best would be to
attach data to the bug report - in this case a relax save state just
prior to the bug occurring.  Could you also include the output of the
'relax --info' command?

Cheers,

Edward


On 18 November 2014 00:06, Prem Raj Joseph  wrote:
> Hello all,
>
> I was using the GUI version of the software to run the tutorial available
> in the manual for analysis of relaxation dispersion.
> When i execute the run I get the following error
>
> RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov 17
> 10:50:08 2014)' already exists.
>
> Not sure where the error is arising from. Any help is greatly appreciated.
>
> Thanks
>
> Prem
>
> Department of Biochemistry and Molecular Biology
> Sealy Center for Structural Biology and Molecular Biophysics
> 5.142 Medical Branch  Building
> University of Texas Medical Branch
> Galveston, TX 77555-1055
> Lab: 409-772-2181
> Cell: 409-354-8536
>
> !!
> Error analysis
> ==
>
> Skipping the error analysis as it has already been performed.
>
> relax> relax_disp.r1_fit(fit=False)
>
>
>
> -
> - The 'R2eff' model -
> -
>
>
> relax> pipe.copy(pipe_from='origin - relax_disp (Mon Nov 17 10:50:08
> 2014)', pipe_to='R2eff - relax_disp (Mon Nov 17 10:50:08 2014)',
> bundle_to='relax_disp (Mon Nov 17 10:50:08 2014)')
> Exception raised in thread.
>
> Traceback (most recent call last):
>   File "/home/prem/programs/relax-3.3.2/gui/analyses/execute.py", line 87,
> in run
> self.run_analysis()
>   File "/home/prem/programs/relax-3.3.2/gui/analyses/auto_relax_disp.py",
> line 726, in run_analysis
> Relax_disp(pipe_name=self.data.pipe_name,
> pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
> models=self.data.models, grid_inc=self.data.inc,
> mc_sim_num=self.data.mc_sim_num, exp_mc_sim_num=self.data.exp_mc_sim_num,
> pre_run_dir=self.data.pre_run_dir,
> mc_sim_all_models=self.data.mc_sim_all_models,
> insignificance=self.data.insignificance,
> numeric_only=self.data.numeric_only, r1_fit=self.data.r1_fit)
>   File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py", line
> 137, in __init__
> self.run()
>   File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py", line
> 614, in run
> self.interpreter.pipe.copy(pipe_from=self.pipe_name,
> pipe_to=model_pipe, bundle_to=self.pipe_bundle)
>   File "/home/prem/programs/relax-3.3.2/prompt/uf_objects.py", line 225, in
> __call__
> self._backend(*new_args, **uf_kargs)
>   File "/home/prem/programs/relax-3.3.2/pipe_control/pipes.py", line 191,
> in copy
> raise RelaxPipeError(pipe_to)
> RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov 17
> 10:50:08 2014)' already exists.
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
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Re: C modules not compiled

[Edward d'Auvergne]

Hi Mark,

I would also recommend that you sign up for the relax-announce mailing
list (https://mail.gna.org/listinfo/relax-announce/).  This list only
receives a few emails per year (see
http://news.gmane.org/gmane.science.nmr.relax.announce), and it is
used almost exclusively for announcing new relax versions, for example
relax 3.3.2 which I am in the process of releasing now (see
http://www.nmr-relax.com/download.html).  Since relax 3.2.3, there
have been the following releases:

http://wiki.nmr-relax.com/Relax_3.3.0
http://wiki.nmr-relax.com/Relax_3.3.1
http://wiki.nmr-relax.com/Relax_3.3.2

That last link will appear later today.  If you are performing either
a model-free or relaxation dispersion analysis, I would highly
recommend that you upgrade to relax 3.3.2 to obtain all the bug fixes
and Troels' huge relaxation dispersion speed ups
(http://wiki.nmr-relax.com/Relax_3.3.0).

Regards,

Edward


On 14 November 2014 10:19, Edward d'Auvergne  wrote:
> Hi Mark,
>
> Welcome to the relax mailing lists!  The problem you see could be due
> to a number of factors.  Firstly, could you check if you have the
> compiled file present on your system:
>
> $ ls -alh /usr/local/relax/target_functions/relax_fit.so
> $ file /usr/local/relax/target_functions/relax_fit.so
>
>
> If the file is there, then maybe you have a Python version problem.
> The C module was compiled using Python 2.7.  Normally this will then
> work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux
> set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4
> that I regularly check this with).  You can check this by running
> relax and typing:
>
> relax> import target_functions.relax_fit
>
>
> For example in Python 3, this gives the error:
>
> relax> import target_functions.relax_fit
> Traceback (most recent call last):
>   File "", line 1, in 
> ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so:
> undefined symbol: Py_InitModule4_64
>
>
> Maybe you will see something similar.  In any case you have two
> alternatives.  The first is to upgrade Python, if the relax_fit.so
> file exists, though this can be a painful and dangerous task on Linux
> systems (you can change the base 'relax' file to point to a different
> alternative Python version if you wish).  The second is as Troels
> suggests.  Install the scons program, the Python headers, and then
> just run 'scons' as root in the /usr/local/relax directory to compile
> the module yourself.
>
> Note that you only need this C module for fitting exponential curves
> for the R1, R2, or relaxation dispersion analyses.
>
> Regards,
>
> Edward
>
>
>
>
>
> On 14 November 2014 01:05, Troels Emtekær Linnet  wrote:
>> Hi.
>>
>> Try just write scons
>>
>> But this should only be for the source code.
>>
>> The packaged versions should already have the compiled C code in it.
>>
>> So this is weird.
>>
>> Can you run
>> relax - d
>> and post it here?
>>
>> Best
>> Troels
>> On 13 Nov 2014 22:34, "Maciejewski,Mark W."  wrote:
>>
>>> Hello,
>>>
>>> I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine
>>> except for the error:
>>> "ImportError: relaxation curve fitting is unavailable, the corresponding C
>>> modules have not been compiled."
>>>
>>> I installed relax using the command:
>>> scons install
>>>
>>> I have searched the archives and see that others have had similar
>>> problems, but cannot find a solution that works for me.
>>>
>>> Any suggestions on how to install or compile the C modules?
>>>
>>> Below is the output from "relax -info"
>>>
>>> Thanks,
>>> Mark
>>>
>>>
>>> [nmradmin@nmrbox_wisc ~]$ relax --info
>>>
>>>
>>>
>>> relax 3.2.3
>>>
>>>   Molecular dynamics by NMR data analysis
>>>
>>>  Copyright (C) 2001-2006 Edward d'Auvergne
>>>  Copyright (C) 2006-2014 the relax development team
>>>
>>> This is free software which you are welcome to modify and redistribute
>>> under the conditions of the
>>> GNU General Public License (GPL).  This program, including all modules, is
>>> licensed under the GPL
>>> and comes with absolutely no warranty.  For details type 'GPL' within the
>>> relax prompt.
>>>
>>> Assistance in 

Re: C modules not compiled

[Edward d'Auvergne]

Hi Mark,

Welcome to the relax mailing lists!  The problem you see could be due
to a number of factors.  Firstly, could you check if you have the
compiled file present on your system:

$ ls -alh /usr/local/relax/target_functions/relax_fit.so
$ file /usr/local/relax/target_functions/relax_fit.so


If the file is there, then maybe you have a Python version problem.
The C module was compiled using Python 2.7.  Normally this will then
work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux
set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4
that I regularly check this with).  You can check this by running
relax and typing:

relax> import target_functions.relax_fit


For example in Python 3, this gives the error:

relax> import target_functions.relax_fit
Traceback (most recent call last):
  File "", line 1, in 
ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so:
undefined symbol: Py_InitModule4_64


Maybe you will see something similar.  In any case you have two
alternatives.  The first is to upgrade Python, if the relax_fit.so
file exists, though this can be a painful and dangerous task on Linux
systems (you can change the base 'relax' file to point to a different
alternative Python version if you wish).  The second is as Troels
suggests.  Install the scons program, the Python headers, and then
just run 'scons' as root in the /usr/local/relax directory to compile
the module yourself.

Note that you only need this C module for fitting exponential curves
for the R1, R2, or relaxation dispersion analyses.

Regards,

Edward





On 14 November 2014 01:05, Troels Emtekær Linnet  wrote:
> Hi.
>
> Try just write scons
>
> But this should only be for the source code.
>
> The packaged versions should already have the compiled C code in it.
>
> So this is weird.
>
> Can you run
> relax - d
> and post it here?
>
> Best
> Troels
> On 13 Nov 2014 22:34, "Maciejewski,Mark W."  wrote:
>
>> Hello,
>>
>> I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine
>> except for the error:
>> "ImportError: relaxation curve fitting is unavailable, the corresponding C
>> modules have not been compiled."
>>
>> I installed relax using the command:
>> scons install
>>
>> I have searched the archives and see that others have had similar
>> problems, but cannot find a solution that works for me.
>>
>> Any suggestions on how to install or compile the C modules?
>>
>> Below is the output from "relax -info"
>>
>> Thanks,
>> Mark
>>
>>
>> [nmradmin@nmrbox_wisc ~]$ relax --info
>>
>>
>>
>> relax 3.2.3
>>
>>   Molecular dynamics by NMR data analysis
>>
>>  Copyright (C) 2001-2006 Edward d'Auvergne
>>  Copyright (C) 2006-2014 the relax development team
>>
>> This is free software which you are welcome to modify and redistribute
>> under the conditions of the
>> GNU General Public License (GPL).  This program, including all modules, is
>> licensed under the GPL
>> and comes with absolutely no warranty.  For details type 'GPL' within the
>> relax prompt.
>>
>> Assistance in using the relax prompt and scripting interface can be
>> accessed by typing 'help' within
>> the prompt.
>>
>> ImportError: relaxation curve fitting is unavailable, the corresponding C
>> modules have not been compiled.
>>
>> Processor fabric:  Uni-processor.
>>
>>
>> Hardware information:
>> Machine: x86_64
>> Processor:   x86_64
>> Processor name:  Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
>> Endianness:  little
>> Total RAM size:  3832 Mb
>> Total swap size: 3967 Mb
>>
>> Operating system information:
>> System:  Linux
>> Release: 2.6.32-504.1.3.el6.x86_64
>> Version: #1 SMP Tue Nov 11 17:57:25 UTC 2014
>> GNU/Linux version:   CentOS 6.6 Final
>> Distribution:centos 6.6 Final
>> Full platform string:
>> Linux-2.6.32-504.1.3.el6.x86_64-x86_64-with-centos-6.6-Final
>>
>> Python information:
>> Architecture:64bit ELF
>> Python version:  2.6.6
>> Python branch:   tags/r266
>> Python build:r266:84292, Jan 22 2014 09:42:36
>> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7

Re: Reg : Input files for model free analysis

[Edward d'Auvergne]

Dear Srinivasa,

If you search the BMRB database, there is a lot of published
relaxation data (and model-free results) deposited there.  This type
of data is not distributed with relax, as the BMRB is the correct
place to deposit data, and the relax bmrb.read user function will read
all the data out of the BMRB files.

However if you really need, you might be able to use data in the
directories such as
test_suite/shared_data/diffusion_tensor/ellipsoid/.  You could load
the relaxation data and use the uniform.pdb structure.  But I don't
know how far you will get.  If you are worried about using relax, just
run the graphical user interface (GUI) by running relax as:

$ relax --gui

If you use the tutorial in the relax manual
(http://www.nmr-relax.com/manual/new_protocol_in_GUI.html), but using
your own data, it should be very simple to complete an analysis.

Regards,

Edward



On 10 October 2014 23:29, srinivas penumutchu
 wrote:
> Dear Relax users,
>
> I am new to use Relax software , I want input files of model free analysis
> to practice on Relax software , it would be great help to me if you can
> input files to use the relax ?
>
> Thanking you for great help
>
> --
>
>
> *Best Regards *
>
>
>
>
>
>
>
> *Srinivasa Rao PenumutchuResearch Scholar Protein NMR Lab , II floor-218
> Department of Chemistry National Tsing Hua University, Hsinchu, Taiwan. Ph:
> 886357151-35605,M:+886-912894534 ,   *
>
> *  Email- penumutchu.srini...@gmail.com  *
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users

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Re: Regarding Relax-3.3.0 NMR installation

[Edward d'Auvergne]

Hi Arun,

If you run the command:

$ relax __gui

this will do nothing.  The correct command is:

$ relax --gui

There is also no 'model_free' command line option, so running the following
will result in an error:

$ relax model_free

If this does not help, could you please run:

$ relax -i --tee relax_info.log

These commands will all have to be executed within the Windows Command
Prompt or the Power Shell.  Which are you using?  You will then have a file
called 'relax_info.log' in the directory you ran relax from.  This should
run from any directory.  Could you then open that file in Notepad, copy the
text, and put it into an email.  It would also be extremely useful if you
typed out the exact error messages in full so that they, and the problem,
can be identified.  Actually, let me replace 'extremely useful' with
'absolutely essential' there ;)

Cheers,

Edward



On 16 September 2014 14:25, Arun Gupta  wrote:

> Hi
>
>
>Thanks for your reply. Since I wasn’t able to unzip the folder in the
> C:/ program files (x86) , I have unzipped relax-3.3.0
>  folder in the E :/ folder and pasted the relax-3.3.0 folder in C:/
> program files (x86) . The typing of relax command in relax3.3.0 folder
>  or any other directory launches the relax and its start to run in script
> mode. However the typing of further commands such as relax __gui  and
> model_free
> when running in relax-3.3.0 folder or from any  other folder only shows
> errors like invalid syntax or relax is not defined . Some of the basic
> commands for testing  relax installation
>  work fine such as Hello world mentioned in manual. For wxpython I have
> installed thewxPython3.0-win32-py27
> <http://downloads.sourceforge.net/wxpython/wxPython3.0-win32-3.0.1.1-py27.exe>
> and also have installed nessy and it seems to work fine with installed
> wxpython3.0.
>
>
>
>  Looking forward for your suggestions
>   *Regards*
>
> *Arun*
>
>
>
>   On Monday, September 15, 2014 12:37 PM, Edward d'Auvergne <
> edw...@nmr-relax.com> wrote:
>
>
> Dear Arun,
>
> Welcome to the relax mailing lists.  The unzipping to the "C:\program
> files" problem you see is not relax specific.  This can sometimes
> happen due to Windows security settings.  A quick internet search will
> show innumerable instances of Windows users with the same issue.
>
> As for the GUI, how to you run it?  Do you run relax using:
>
> $ relax --gui
>
> It could be that wxPython is not set up correctly.  Could you run the
> command:
>
> $ relax -i --tee relax_info.log
>
> This will output a lot of information about your setup and might
> indicate what the problem is.  It will also create the relax_info.log
> file which is easier for Windows uses to copy the text from.  Could
> you copy and paste the contents of that into an email?  Please do not
> attach a file to the mailing list message - this will be automatically
> stripped out of the message so it will not be seen.  A good test that
> wxPython is working is to also download the demo files
> (http://www.wxpython.org/download.php#msw).  These must be of the same
> version as your wxPython installation.  If you cannot run the demo,
> then the problem is with wxPython and not relax.  I hope this helps.
>
> Regards,
>
> Edward
>
>
> P. S.  Sorry for the late reply.  My email system thought your email
> was spam, so I didn't see it until today.
>
>
> On 8 September 2014 23:32, Arun Gupta  wrote:
> >
> >
> > Hi
> >
> > I have tried to  install Relax NMR software on my
> > Windows 8 O.S with Python2.7.8 . However when I try to unzip the
> relax-3.3.0
> > zipped folder to program files. I get message access denied although I
> am trying
> > to install administrator settings. However  the zip file can be
> unzipped in
> > other folder and copied to C:/ folder but the relax-3.3.0 GUI interface
> doesn't
> >  come on model_free. command. Can you suggest solution to these
> > issues
> >
> > Regards
> >
> > Arun
>
> > ___
> > relax (
> http://www.nmr-relax.com/)
> >
> > This is the relax-users mailing list
> > relax-users@gna.org
> >
> > To unsubscribe from this list, get a password
> > reminder, or change your subscription options,
> > visit the list information page at
> > https://mail.gna.org/listinfo/relax-users
>
>
>
>
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Re: Question on choosing relaxation dispersion models for proteins

[Edward d'Auvergne]

Hi Chung-ke,

It is quite confusing with the huge spectrum of relaxation dispersion
models that can be found in the literature covering all different
relaxation dispersion conditions.  However you should only use models
when you know that they apply to your system.  For the Ishima and
Torchia model (http://wiki.nmr-relax.com/IT99), this has the condition
that pA >> pB, which is quite different to the Carver and Richards
model (http://wiki.nmr-relax.com/CR72) or Nikolai Skrynnikov's
expanded numerical model
(http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded).  You really need
to read the primary reference for any model you use.  For example in
the Ishima and Torchia paper, you will find the text:

"Equation 4 predicts values of Rex that agree with those calculated
using Equation 3, within 15%, for all values of δωτex, when p1/p2 <
0.15."

Equation 3 is the CR72 model and equation 4 is the IT99 model.

You should note that the IT99 model is what is known in the field of
mathematical modelling as a 'flexible model'.  It is more able to
adapt and fit to the data more than the other models.  However that
does not mean that it is better.  But it will be chosen more than
non-flexible models using Akaike's Information Criterion (AIC) model
selection.  There are more advanced techniques in the field of model
selection which deal with such flexible models, for example ICOMP (the
Information Complexity Criterion).  But these are not implemented in
relax for now.  For an introduction to model selection in NMR, see my
model-free model selection paper at
http://dx.doi.org/10.1023/A:1021902006114.  There are some good
textbook references in there which explain all of this, and why ICOMP
would probably not select the IT99 model.

However, I would guess that your aim is not to study model selection
or the IT99 model results, but just to perform a dispersion analysis.
The IT99 paper quote above also indicates that this is a very
approximate model, and is probably not what you are looking for.  If
this is the case, don't use the IT99 model!  Note that the model
selection is provided mainly to see if the dispersion model fits the
data better than the 'No Rex' model - i.e. it is used to judge if the
dispersion process is statistically significant.  You cannot compare
the different dispersion models using model selection as the domain of
validity of most models do not match, they are for different
dispersion conditions, and scientific logic always trumps model
selection.

Anyway, a general rule of thumb is that if you are not sure that a
model is suited for your system, then it probably isn't.  You should
also take note of Troels' suggestion of Andy Baldwin's recent model
(http://wiki.nmr-relax.com/B14) which can replace the CR72 model.  If
it is all too confusing, then the defaults of simply the 'R2eff', 'No
Rex', 'CR72', and 'NS CPMG 2-site expanded' models should be used.
And maybe you should set the NUMERIC_ONLY value to True so that you
only compare the 'No Rex' and numeric CPMG model.  I hope this helps.

Regards,

Edward



On 15 September 2014 04:56, Chung-ke Chang  wrote:
> Dear all,
>
> I’ve been tearing my hair out trying to figure out how to choose relaxation 
> dispersion models for a particular protein. I’ve ran into a case where many 
> residues are fit to the ‘IT99’ model, but did not fit to the ’NS CPMG 2-site 
> expanded’ model (relax doesn’t even bother to show the Chi2 and AIC in the 
> log file). If I understand correctly, the ’NS CPMG 2-site expanded’ model is 
> an exact numerical solution based on the original Bloch-McConnell equations, 
> whereas ‘IT99’ is an analytical approximation. I would expect that whatever 
> can be fit with the ‘IT99’ model should also be able to fit to the ’NS CPMG 
> 2-site expanded’ model since they seem to share the same restrictions (pA > 
> pB). Or am I missing something?
>
> Cheers,
>
> Chung-ke
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Re: Regarding Relax-3.3.0 NMR installation

[Edward d'Auvergne]

Dear Arun,

Welcome to the relax mailing lists.  The unzipping to the "C:\program
files" problem you see is not relax specific.  This can sometimes
happen due to Windows security settings.  A quick internet search will
show innumerable instances of Windows users with the same issue.

As for the GUI, how to you run it?  Do you run relax using:

$ relax --gui

It could be that wxPython is not set up correctly.  Could you run the command:

$ relax -i --tee relax_info.log

This will output a lot of information about your setup and might
indicate what the problem is.  It will also create the relax_info.log
file which is easier for Windows uses to copy the text from.  Could
you copy and paste the contents of that into an email?  Please do not
attach a file to the mailing list message - this will be automatically
stripped out of the message so it will not be seen.  A good test that
wxPython is working is to also download the demo files
(http://www.wxpython.org/download.php#msw).  These must be of the same
version as your wxPython installation.  If you cannot run the demo,
then the problem is with wxPython and not relax.  I hope this helps.

Regards,

Edward


P. S.  Sorry for the late reply.  My email system thought your email
was spam, so I didn't see it until today.


On 8 September 2014 23:32, Arun Gupta  wrote:
>
>
> Hi
>
> I have tried to  install Relax NMR software on my
> Windows 8 O.S with Python2.7.8 . However when I try to unzip the relax-3.3.0
> zipped folder to program files. I get message access denied although I am 
> trying
> to install administrator settings. However  the zip file can be  unzipped in
> other folder and copied to C:/ folder but the relax-3.3.0 GUI interface 
> doesn't
>  come on model_free. command. Can you suggest solution to these
> issues
>
> Regards
>
> Arun
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Re: How does the error intensity analysis handle both specification of baseplane RMSD and partly repeated spectrum?

[Edward d'Auvergne]

Hi Troels,

Currently you can only choose one technique or the other.  You will
see this in the algorithm for choosing between the different
techniques in the pipe_control.spectrum.error_analysis() function
(http://www.nmr-relax.com/api/3.3/pipe_control.spectrum-pysrc.html#error_analysis).
Replicates come first, if present, and that will be used for error.
This calls __errors_repl().  If no replicates exist, then either
__errors_height_no_repl() or __errors_vol_no_repl() are called.
Coming up with an algorithm that does a mixture of both will be
difficult.  And it will also be complicated to explain the behaviour
to the user, though that is currently done using printouts.

Regards,

Edward

On 12 September 2014 14:22, Troels Emtekær Linnet  wrote:
> Dear Edward.
>
> I was wondering how relax handles the error intensity analysis,
> where one both specify the baseplane RMSD and and one also have partly
> repeated spectrums?
>
>
> For example you have recorded for 10 time series.
>
> You measure the baseplane RMSD for each spectrum.
>
> You have repeated spectrum 1,2 and 7,8.
>
> You specify all this to relax.
>
> Best
> Troels
>
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Re: Relaxation dispersion clustering calculation time

[Edward d'Auvergne]

Hi Chung-ke,

The aim of relax is to support absolutely every NMR dynamics theory in
existence!  For the relaxation dispersion analysis section of relax,
this means supporting all published models for the dispersion data,
and all parametric restrictions of these models.  Many of the
dispersion models have been derived with the assumption that R20A and
R20B are different, the Carver and Richards model is a good example of
this (http://wiki.nmr-relax.com/CR72_full).  These are the '* full'
models in relax.  However in the literature the parametric restriction
R20A = R20B (= R20) is almost always used.  For the analytic models
this can significantly simplify the equations, whereas for the numeric
models the equations do not change.  In both cases, two dimensions of
the the optimisation space collapse into one and the optimisation
problem massively simplifies.  That is why in relax we also provide
the collapsed models (those with the ' full' part of the label
removed).

It is true most literature data is not suitable for the '* full'
models.  That is why they are not turned on by default in the GUI or
listed in the sample scripts.  From memory though, there are cases
whereby the measured data is of high enough quality and collected on
enough magnets that the R20A != R20B assumption can be made.  I cannot
remember the reference(s), but it shouldn't be too hard to find.
Anyway, the full R20A != R20B models are provided in relax for a
number of reasons:

  - The rare cases whereby the data is good enough.
  - Academic studies.
  - Future developments could significantly improve the quality of
measured dispersion data so that the R20A != R20B assumption can be
regularly made.
  - Chemists have a different perspective on life compared to
biologists.  Small organic molecules make the R20A vs. R20B
distinction much, much easier.

I hope it is now clearer why there are these models in relax.

Regards,

Edward




On 10 September 2014 15:27, Chung-ke Chang  wrote:
> Dear Edward and Troels,
>
> Thank you all for the help! We are currently testing the new version of relax 
> (yes, we are using the “normal” release), and making sure it plays along 
> nicely with other software - we have a plethora of different python versions, 
> which the system manager is doing his best to avoid interfering with each 
> other. I am curious about one thing though: If the ‘CR72 full’ model has not 
> been used in any published studies, then is there any reason to include it 
> when trying to fit “real-world” data? It seems that Troels is implying that 
> “real-world” data is too noisy to obtain meaningful fitting parameters from 
> the model. Or am I misunderstanding something?
>
> Cheers,
>
> Chung-ke
>
> On Sep 9, 2014, at 8:56 PM, Edward d'Auvergne  wrote:
>
>> Hi Chung-ke,
>>
>> The only way to find out about new relax releases is the
>> relax-announce mailing list
>> (http://news.gmane.org/gmane.science.nmr.relax.announce).  Some relax
>> users were signed up for the freecode announcements
>> (http://freecode.com/projects/nmr-relax), but freecode has
>> unfortunately shut down (http://freecode.com/about).
>>
>> For the version you are currently using, note that this is the
>> repository version of relax installed by the superuser.  You should
>> make sure you use the normal releases, as the repository version can
>> sometimes be in a broken or buggy state as development occurs.  You
>> can also have a copy in your home directory by typing:
>>
>> $ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk
>> $ cd relax-trunk
>> $ scons
>>
>> If you already have a repository version on your system, these
>> commands should just work.  But you should only use the repository
>> version if you would like a bug fix and cannot wait until the next
>> relax release.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> On 9 September 2014 10:37, Chung-ke Chang  wrote:
>>> Dear Troels and Edward,
>>>
>>> Thank you for the pointers. I was not aware that a new version was out last
>>> week, so I’ve asked the IT people to install it on our cluster. Below is the
>>> output from ‘relax -i’:
>>>
>>> [chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i
>>>
>>>
>>>
>>>  relax repository checkout r24533
>>> svn://svn.gna.org/svn/relax/trunk
>>>
>>>  Molecular dynamics by NMR data analysis
>>>
>>> Copyright (C) 2001-2006 Edward d'Auvergne
>>> Copyright (C) 2006-2014 the relax development team
&g