from:"Edward d'Auvergne"

Hi Troels,

Welcome to the relax mailing lists.  For now the answer to your
question is, unfortunately, no - relax does not officially support
relaxation dispersion.  The analysis you are running is simple two
parameter exponential curve-fitting
(http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html).  This
can be used to find the R2eff or R1rho values if you have measured the
full exponential curves, but otherwise you cannot perform a dispersion
analysis with this.

This may not be of use for you at the moment, but note that relax has
unofficial and incomplete support for dispersion analyses (both
CPMG-type and R1rho-type data sets).  As relax is open source, there
are many NMR spectroscopists who have added code to relax (for example
see http://gna.org/project/memberlist.php?group=relax).  An initial
implementation of the relaxation dispersion analysis was added to a
relax branch back in 2009 by Sebastian Morin
(http://thread.gmane.org/gmane.science.nmr.relax.devel/1728).  But as
this was not completed at the time, it was never merged back into the
relax main line (the source code where official relax releases come
from).  I have recently restored the branch to a partially working
state and added a graphical interface for the analysis - mainly for my
own purposes (http://svn.gna.org/viewcvs/relax/branches/).  So at some
point in the near future relax will be able to perform the analyses
you are interested in.

As relax is open source, if you are interested and adventurous enough
you are most welcome to help in the development.  Even if you do not
know how to code, there are many other things which can be done.  For
example calculating the partial derivatives of the analytic solutions
to obtain the gradients and Hessians so that with relax you can have
access to far more powerful optimisation algorithms than any of the
other dispersion software has access to.  Or to create test data
whereby the solution is know, or to collect the input and output test
data from published results.  If you have the subversion version
control software installed, you can obtain the code by typing either:

$ svn co svn://svn.gna.org/svn/relax/branches/relax-disp

or:

$ svn co http://svn.gna.org/svn/relax/branches/relax-disp

If you are more interested in quickly performing the analysis, I would
point you to Dr. Flemming Hansen's CATIA program:

http://www.biochem.ucl.ac.uk/hansen/catia/ (the old page is
http://pound.med.utoronto.ca/~flemming/catia/).

This performs numerically integration of the Bloch-McConnell
equations, so not the optimisation of the analytic solutions of
Meiboom, Richard-Carver, etc.  It is also only for CPMG-type data
rather than R1rho, whereas the relax branch will handle both.  I hope
this information helps.

Regards,

Edward




On 30 April 2013 18:40, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Dear relax users.

 I am looking into different NMR programs to fit
 relaxation data for CPMG relaxation dispersion experiments and T1rho.

 Essentially, I am looking for programs for which can fit functions, which
 for example nessy provide:
 http://home.gna.org/nessy/reference.html
 The Meiboom equation or Richard-Carver equation

 Nessy is very buggy, and I am looking for a replacement.

 I should be able to:
 R2eff = -1.0/time_T2*log(Intensity/averageZero)

 ncyc_arr=[28, 0, 4, 32, 60, 2, 10, 16, 8, 20, 50, 18, 40, 6, 12, 0, 24]
 time_T2 = 0.06 second
 nu = ncyc_arr[i]/time_T2

 R2cpmg_slow:
 tau_cpmg = 1.0/(4*nu)
 R2eff = R2+ka*(1.0-sin(Domega*tau_cpmg)/(Domega*tau_cpmg))


 I have followed the tutorial in the homepage manual:

 Can relax analyse these kinds of experiments?
 Should i provide the: relax_fit.relax_time(time to be equal tau_cpmg ?
 I put in time_T2, even though its wrong. I just wanted to try the program.
 :-)

 
 Script for relaxation curve fitting.
 # Create the 'rx' data pipe.
 pipe.create('rx', 'relax_fit')
 ## Load the backbone amide 15N spins from a PDB file.
 pdbfile=False
 if pdbfile:
 structure.read_pdb(pdbfile)
 structure.load_spins(spin_id='@N')
 else:
 molecule.create(mol_name='protein', mol_type='protein')
 residue.create(res_num=2, res_name='VAL')
 spin.create(res_num=2, spin_name='N')
 residue.create(res_num=3, res_name='PHE')
 spin.create(res_num=3, spin_name='N')
 residue.create(res_num=4, res_name='GLY')
 spin.create(res_num=4, spin_name='N')
 residue.create(res_num=5, res_name='ARG')
 spin.create(res_num=5, spin_name='N')
 residue.create(res_num=6, res_name='CYS')
  and so on

 ## Loop over the spectra intensities. Relaxation times should be in seconds.
 readint=True
 if readint:
 spectrum.read_intensities(dir='relax', file='proc_list.txt.0int',
 spectrum_id='0_0.0', int_method='point sum', heteronuc='N', proton='HN',
 int_col=3)
 relax_fit.relax_time(time=0.06, spectrum_id='0_0.0')
 spectrum.read_intensities(dir='relax',

Re: Missing data for spin system and compatibility in GUI

Hi Nav,

I wouldn't worry about this.  I don't think there is a single person
in history who has collected perfect relaxation data the first time.
If someone says they have, I definitely would not believe them!  Just
make sure you handle both temperature compensation (single-scan
interleaving and temperature compensation blocks) and temperature
control (checking every experiment on every spectrometer with
MeOH/Ethylene glycol).  Unfortunately the paper from the Gooley lab
describing this is not published yet.  But all the details are
described in the relax manual, so maybe the relax papers might be a
possible citation ;)

Regards,

Edward




On 2 May 2013 11:13, Navratna Vajpai navratna.vaj...@gmail.com wrote:
 Hi All,

 yes there is temperature difference on two different spectrometers. i will
 re calibrate and possibly re-do the experiments.

 Many thanks for all the suggestions.

 Best,
 Nav


 On Tue, Apr 30, 2013 at 4:32 PM, Edward d'Auvergne edw...@nmr-relax.com
 wrote:

 Hi Nav,

 Martin is spot on here.  The temperature control and temperature
 calibration has been a topic much discussed on the relax mailing
 lists.  For example, here are some threads where you can find out more
 information, if you wish:

 http://thread.gmane.org/gmane.science.nmr.relax.user/83
 http://thread.gmane.org/gmane.science.nmr.relax.user/273/focus=274
 (this is Chris MacRaild's response to a message by Seb Morin)
 http://thread.gmane.org/gmane.science.nmr.relax.user/1121
 http://thread.gmane.org/gmane.science.nmr.relax.user/1419
 http://thread.gmane.org/gmane.science.nmr.relax.user/1368 (this one is
 from Martin)
 http://thread.gmane.org/gmane.science.nmr.relax.user/1397 (a
 continuation of the previous thread)

 You need to click on all the messages in the thread to follow them.
 There are many more threads on this area, but I don't have the time to
 find them all right now.  The following message might be of
 significant help for you:

 http://thread.gmane.org/gmane.science.nmr.relax.user/1419/focus=1423

 Firstly note that if you have a temperature problem, this will not be
 solved by looking at a single field strength as it is a problem
 between experiments on the same spectrometer.  So even if you perform
 an analysis with data from a single field strength, the R1 data might
 be up to 2 degrees warmer or colder than the R2, and the same problem
 will occur to a different degree (or direction) on the second
 spectrometer.  Any analysis using such data will be meaningless, as
 this will have a large effect on the diffusion tensor.  Considering
 that the diffusion tensor is the major contributor to liquid state
 relaxation, the internal dynamics can contribute 20% or less (see the
 original model-free papers for these numbers), then any internal
 dynamics will be severely distorted, possibly hidden, and artificial
 motions will appear.  I would recommend you look at this section of
 the relax manual for more temperature related details:

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

 As for relax supporting an analysis at a single field strength, there
 is nothing stopping you from performing such analysis.  relax is
 designed with flexibility in mind, so you can perform your model-free
 analysis any way you can imagine.  With the minimisation settings, you
 can replicate the exact results from Art Palmer's Modelfree, from
 Dasha, or from Tensor2.  However note that I have not written any
 scripts or GUI to handle this situation, as I have no interest to.  So
 you would need to write the script yourself.  I would then recommend
 looking at the file 'auto_analyses/dauvergne_protocol.py' to get an
 idea of how to implement a full model-free protocol.  It is quite big
 because of the iterative optimisation of the model-free parameters,
 then model elimination, then model selection, and finally diffusion
 tensor optimisation, with convergence testing.  These steps, even for
 single field strength data, need to be iterated until convergence.
 This can take up to 15 iterations.  You will also need to decide how
 to determine your initial diffusion tensor estimate - and relax can
 perform this as well.

 But note that you should be aware of of the problems discovered by
 Schurr et al., 1994 and Tjandra et al., 1996 of the artificial
 motions.  For example see:

 http://thread.gmane.org/gmane.science.nmr.relax.user/326/focus=332

 Korzhnev's review (I don't have the reference at hand) and my paper
 (http://dx.doi.org/10.1039/b702202f, this has the Korzhnev reference
 in it) cover all of the problems you will encounter and hopefully
 convince you that an analysis of single field strength data would only
 be useful for perfectly isotropic systems (which is never possible due
 to water shell differences around the system) which have no
 significant internal motion (but note that if you see no motion with
 single field strength data, that does not mean that there is no
 motion).

 I hope this helps

Re: Is it possible to analyse CPMG experiments with relax?

Hi,

Its great that you have an interest and know Python - you are in a
perfect position to join as a relax developer!  See below for more
responses:


 Thank you for your generous email, which helped a-lot.

You're welcome!


 I am happy to see the active development, and I would be more than happy to
 join in.
 I am quite good in python programming, and are confident i revision
 programs as svn and git.
 And I have courses in scientific computing, so I think i get along quite
 good.

I would recommend you have a read of the relax open source
infrastructure chapter of the relax manual
(http://www.nmr-relax.com/manual/Open_source_infrastructure.html) and,
more importantly, the development chapter of the relax manual
(http://www.nmr-relax.com/manual/relax_development.html).  The PDF
version of the manual is much easier to read
(http://download.gna.org/relax/manual/relax.pdf).  These chapters
describe in full detail everything you would ever need as a relax
developer.  Note that relax is a very mature project, so learning how
to code in such an environment to avoid breaking the rest of the
program will give you quite a different skill set.

You might also be interested in learning about the minfx project that
relax uses for optimisation (https://gna.org/projects/minfx/).  This
originated as a relax package as the scipy optimisers all contained
fatal bugs back in 2003 (I'm not sure they have been fixed as the
original developers were MIA even back then and I think have never
returned).  But it was spun out into its own software distribution.


 My reason for my interest, is that I think I should change my working
 habits, to something more effect full.

 My work-flow at the moment, is this.

 1) CPMG/T1-rho experiment acquisition with NLS, through VnmrJ.

I have to warn you here that non-linear sampling is notoriously bad
for measuring high precision NMR parameters such as relaxation data.
I would recommend avoiding this technique if you can.  It is great for
low precision data required for assignment, for example, but not so
good for the high precision data measurements.


 2) Data reconstruction in qMDD.
 (3) Main peak positioning in CcpNmr  Analysis.)
 4) Small peak adjustment, control in SPARKY.
 5) Point sum integration in with: seriesTab with: -dx 1 -dy 1
 6) Integration analysis in gnuplot/IgorPro,Originlab.
 The use of IgorPro,Originlab have been used because of easy use of the
 global fitting routine, but pose a problem, since
 we only have a very few licenses. And I weigh open-source very high. :-)

The way I perform this is a bit different in that I use peak heights
directly from Sparky.


 The last weeks, I have fiddling around my workflow to try something like
 this:
 1) CPMG/T1-rho experiment acquisition with NLS, through VnmrJ.
 2) Data reconstruction in qMDD.
 (3) Main peak positioning in CcpNmr  Analysis.)
 4) Small peak adjustment, control in SPARKY.
 5) Point sum integration in nmrglue, and easy visualization of each
 integration. Preparation of data for fitting.
 6) Global fitting. Either with nessy, relax or with python scipy leastsq.

 Here I tried to make a nessy database, but nessy came out very buggy.
 And I was about to set out for some python scipy fitting after nmrglue.

I am currently the maintainer of the NESSY project, but the types of
bugs reported require significant amounts of coding to solve the
problems.  Unfortunately I don't have the time for this - it could be
a few months of work.  As for nmrglue
(http://code.google.com/p/nmrglue/), this appears quite new and this
is the first time I have heard of it.  It looks like an interesting
project.  I wonder if they use 3-point quadratic integration for
determining the maximum peak height?


 But I had a hard time imagining that NMR software were not already developed
 for this,
 and I was very pleased to see the development of relax, which have not come
 to my attention before.
 And especially the inclusion of the python interpreter, and possibility to
 write scripts, is genius.
 Which is similar to the where the power of pymol is shining through.

Thanks!  I am directing the development of relax to have the maximum
amount of flexibility.  For the basic users who want quick results,
there are the auto-analyses which can be used as blackboxes, giving
the user the best practice analysis.  These are used in the GUI.  For
the medium level users, the user functions (which are special Python
functions which perform a lot of checking of the user input) allow for
advanced scripting.  For the advanced users, the relax API can be used
to build complete new analyses (http://www.nmr-relax.com/api/).  I
have been developing relax so that in the future it can be used by NMR
users as a replacement for Matlab/Mathematica for numerical
operations.  The relax library - the 'lib' package - is a large
collection of NMR specific functions.  For example, have a look at the
rotation matrix module 'lib.geometry.rotations'

Re: Building relax from source using scons and a different python interpretor

Hi Troels,

In the future, for such questions I would recommend asking on the
relax development mailing list (relax-devel att gna.org).  The answer
is complicated as SCons has problems with multiple Python
installations.  You have to have scons installed for the Python
version you are targeting and no other SCons versions present.  I have
managed to get it to work, but the scons must be run with the correct
Python version and also then separately find the correct Python
version for compilations (these are unfortunately not coupled in
SCons).  There is one cheating way and that is to use the
'devel_scripts/manual_c_module.py' script, just modifying it to point
your Python version.  This script is mainly to get around these bad
design issues in SCons for when multiple Python versions are present,
as I have lots of different Python versions compiled into a special
directory for testing relax (every version from 1.0 to 3.3) and SCons
really cannot handle this.

As for using Enthought Python, I don't know how well relax will run in
such an environment.  It'll be interesting to see what happens.

Regards,

Edward


On 2 May 2013 17:26, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Dear Relax users.

 I am trying to build relax, from source, using scons.

 We have the python enthought distribution installed, to solve most of our
 dependencies,
 and we install packages here, so each computer can use this shared
 installation.

 How I can I tell scons, to use python2.7 to build relax?
 I think it tries to use my local python installation, but here I have not
 installed
 minfx, ,wxPython.

 [tlinnet@tomat ~/software]$ cd relax-trunk/
 [tlinnet@tomat relax-trunk]$ scons
 scons: Reading SConscript files ...
 The dependency 'minfx' has not been installed (see
 https://gna.org/projects/minfx/).
 [tlinnet@tomat relax-trunk]$ python2.7
 Enthought Python Distribution -- www.enthought.com
 Version: 7.3-2 (64-bit)

 Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 11 2012, 17:52:16)
 [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
 Type credits, demo or enthought for more information.
 import minfx
 import readline
 import wx
 import numpy
 import scipy

 Best
 Troels


 Troels Emtekær Linnet
 Ved kløvermarken 9, 1.th
 2300 København S
 Mobil: +45 60210234

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Re: Peak list abs spin editor

2013-06-03 Thread Edward d'Auvergne

Hi,

For such questions, it may be better to ask on the relax-users mailing
list as the answer might be useful for other users.  You can see what
is happening with Sparky peak list files in the relax module
lib.software.sparky.  If you specifically look at the
read_list_intensity() function, you will see the lines:

# Skip non-assigned peaks.
if line[0] == '?-?':
continue

This needs to be done in relax as it is not possible to hold data from
such peaks in the relax data store.  The way I handle such a situation
in Sparky is to give all such peaks a temporary or pseudo-assignment,
for example SS1000, SS1001, etc.  Essentially having a special residue
name and numbers starting much higher than the end of your system's
sequence numbering.  These can then be given 'N' and 'HN' labels.  You
would then need to create these spin system within relax prior to
reading the peak lists, and the data will then be handled as normal.
This could either be by creating and then reading in a text file
containing all of these spins with residue numbers and names in
different columns, using individual calls to the spin.create user
function, or within the spin editor window of the GUI (which just
provides access to the graphical version of the spin.create user
function).

For the question about multiple reference spectra, have a look at the
specific_analyses/relax_disp/__init__.py file (in the relax_disp
branch).  Specifically within the calculate() method used for the
fixed time period experiments, you will see the lines:

# Average the reference intensity data and errors.
ref_intensity = average_intensity(spin=spin, frq=frq,
point=None, time=time)
ref_intensity_err = average_intensity(spin=spin,
frq=frq, point=None, time=time, error=True)

# Average the intensity data and errors.
intensity = average_intensity(spin=spin, frq=frq,
point=point, time=time)
intensity_err = average_intensity(spin=spin, frq=frq,
point=point, time=time, error=True)

# Calculate the R2eff value.
spin.r2eff[param_key] =
calc_two_point_r2eff(relax_time=time, I_ref=ref_intensity,
I=intensity)

# Calculate the R2eff error.
spin.r2eff_err[param_key] =
calc_two_point_r2eff_err(relax_time=time, I_ref=ref_intensity,
I=intensity, I_ref_err=ref_intensity_err, I_err=intensity_err)


So you can see that the data from multiple spectra are averaged.  This
relies on the my assumption that this is the logical thing to do.  For
the peak intensity error analysis prior to this, how multiple spectra
are handled depends on what you have measured and whether you have
measured all spectra replicated or only a subset.  This is described
in full detail within the documentation for the current
spectrum.error_analysis user function (see either the help system or
the user manual at
http://www.nmr-relax.com/manual/spectrum_error_analysis.html).

Regards,

Edward



On 3 June 2013 18:55, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi !

 I have been playing around in relax_disp, and wonder.

 Can relax handle un-assigned peaks?
   Assignment w1 w2   Height   Volume
  A101N-A101HN124.571  8.003   0.00E+00   0.00E+00 --
   ?-?124.316  7.962   0.00E+00   0.00E+00 --

 We often have 2-3 un-assigned peaks, which is interesting to carry on
 in our analysis.

 Can you have several reference spectra?
 We have some datasets with 2-3 replicates for the reference spectrum.

 Best


 Troels Emtekær Linnet

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Re: Custom Peak intensity reading

2013-06-04 Thread Edward d'Auvergne

I have to admit, the error message should be made more informative!
However that error statement (line 668 of lib/io.py) cannot be reached
without relax giving many warnings.  The only possibility of reaching
the error without warnings is if the file is empty.  Do you see
warnings which could indicate the problem?  If not, I would suggest
creating a bug report for the problem and attaching a minimal set of
files to be able to reproduce the issue.  It would be best if the
files are truncated to 1-2 spins (and maybe randomised if the data is
to be kept secret).  If it really is a bug, then these files could be
be added to the test suite and turned into a system or GUI test to
catch the problem.

Cheers,

Edward


On 4 June 2013 14:37, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 I have made a custom intensity peak/model file, for easy import in relax.
 The form is:

 protein 10 L 10 N 3.377659e+05 6.362446e+05
 protein 6 V 6 N 1.697771e+06 3.015788e+06
 protein 63 Y 63 N 8.673898e+05 1.726064e+06
 protein 4 Y 4 N 2.339480e+06 4.039142e+06
 protein 67 M 67 N 2.574062e+06 4.313824e+06
 protein 5 E 5 N 1.609356e+06 2.927111e+06
 protein 65 V 65 N 2.179341e+06 4.067343e+06
 protein 38 E 38 N 1.563795e+06 2.921316e+06
 protein 7 N 7 N 1.535896e+06 3.005234e+06
 protein 75 L 75 N 3.578841e+06 6.352595e+06

 This goes fine for model import, with standard settings.

 Start new analysis
 Relaxation dispersion analysis
 Relaxation dispersion experiment type selection
 CPMG, fixed time
 Data pipe set up
 The starting data pipe for the analysis = origin - relax_disp (Mon Jun
 3 17:08:30 2013)
 The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013)

 Click: Spin editor
 Click: Load spins
 Make a test file: test.seq

 Click: From a file containing sequence data
 The file name = test.seq
 The spin ID string = Leave empty
 Free format
 Molecule name column (mol_name_col) = 1
 Residue number column (res_num_col) = 2
 Residue name column (res_name_col) = 3
 Spin number column (spin_num_col) = 4
 Spin name column (spin_name_col) = 5
 You can then rename molecule by, right click Molecule: protein,
 Name the molecule, Set The new molecule name to for example
 Test. Apply, then OK.

 Add spectra
 Click Add

 The file name = test.seq
 The Spectrum ID string: 2,0
 The Intensity column: 6,7
 rest is default

 Error:
 No corresponding data could be found within the file.

 I can import single wise.

 best
 Troels


 Troels Emtekær Linnet

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Re: Custom Peak intensity reading

Hi,

Have you had any luck finding the problem?  I would guess that this
doesn't work as the protein was renamed to something different to that
of the data file, hence you would see messages such as:

relax spectrum.read_intensities(file='test.seq', dir=None,
spectrum_id=None, heteronuc='N', proton='HN', int_method='height',
int_col=6, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, int_col=6, sep=None,
spin_id=None, ncproc=None)
Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for reading.
Generic formatted data file.

RelaxWarning: Cannot find the spin #protein:10@N within the sequence.
RelaxWarning: Cannot find the spin #protein:6@N within the sequence.
RelaxWarning: Cannot find the spin #protein:63@N within the sequence.
RelaxWarning: Cannot find the spin #protein:4@N within the sequence.
RelaxWarning: Cannot find the spin #protein:67@N within the sequence.
RelaxWarning: Cannot find the spin #protein:5@N within the sequence.
RelaxWarning: Cannot find the spin #protein:65@N within the sequence.
RelaxWarning: Cannot find the spin #protein:38@N within the sequence.
RelaxWarning: Cannot find the spin #protein:7@N within the sequence.
RelaxWarning: Cannot find the spin #protein:75@N within the sequence.
RelaxError: No data could be loaded from the peak list

I tried this by copying the data in your post to a file and following
the instructions.  This is normal as the molecule with the name
'protein' no longer exists in the relax data store.  Or did you see
something different?  The RelaxError text you wrote about is slightly
different.

Regards,

Edward


On 4 June 2013 15:10, Edward d'Auvergne edward.dauver...@gmail.com wrote:
 I have to admit, the error message should be made more informative!
 However that error statement (line 668 of lib/io.py) cannot be reached
 without relax giving many warnings.  The only possibility of reaching
 the error without warnings is if the file is empty.  Do you see
 warnings which could indicate the problem?  If not, I would suggest
 creating a bug report for the problem and attaching a minimal set of
 files to be able to reproduce the issue.  It would be best if the
 files are truncated to 1-2 spins (and maybe randomised if the data is
 to be kept secret).  If it really is a bug, then these files could be
 be added to the test suite and turned into a system or GUI test to
 catch the problem.

 Cheers,

 Edward


 On 4 June 2013 14:37, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 I have made a custom intensity peak/model file, for easy import in relax.
 The form is:

 protein 10 L 10 N 3.377659e+05 6.362446e+05
 protein 6 V 6 N 1.697771e+06 3.015788e+06
 protein 63 Y 63 N 8.673898e+05 1.726064e+06
 protein 4 Y 4 N 2.339480e+06 4.039142e+06
 protein 67 M 67 N 2.574062e+06 4.313824e+06
 protein 5 E 5 N 1.609356e+06 2.927111e+06
 protein 65 V 65 N 2.179341e+06 4.067343e+06
 protein 38 E 38 N 1.563795e+06 2.921316e+06
 protein 7 N 7 N 1.535896e+06 3.005234e+06
 protein 75 L 75 N 3.578841e+06 6.352595e+06

 This goes fine for model import, with standard settings.

 Start new analysis
 Relaxation dispersion analysis
 Relaxation dispersion experiment type selection
 CPMG, fixed time
 Data pipe set up
 The starting data pipe for the analysis = origin - relax_disp (Mon Jun
 3 17:08:30 2013)
 The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013)

 Click: Spin editor
 Click: Load spins
 Make a test file: test.seq

 Click: From a file containing sequence data
 The file name = test.seq
 The spin ID string = Leave empty
 Free format
 Molecule name column (mol_name_col) = 1
 Residue number column (res_num_col) = 2
 Residue name column (res_name_col) = 3
 Spin number column (spin_num_col) = 4
 Spin name column (spin_name_col) = 5
 You can then rename molecule by, right click Molecule: protein,
 Name the molecule, Set The new molecule name to for example
 Test. Apply, then OK.

 Add spectra
 Click Add

 The file name = test.seq
 The Spectrum ID string: 2,0
 The Intensity column: 6,7
 rest is default

 Error:
 No corresponding data could be found within the file.

 I can import single wise.

 best
 Troels


 Troels Emtekær Linnet

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Re: Custom Peak intensity reading

 ['protein', '4', 'Y', '4',
 'N', '2.339480e+06', '4.039142e+06'] is invalid, the data is missing.
 RelaxWarning: The sequence data in the line ['protein', '67', 'M',
 '67', 'N', '2.574062e+06', '4.313824e+06'] is invalid, the data is
 missing.
 RelaxWarning: The sequence data in the line ['protein', '5', 'E', '5',
 'N', '1.609356e+06', '2.927111e+06'] is invalid, the data is missing.
 RelaxWarning: The sequence data in the line ['protein', '65', 'V',
 '65', 'N', '2.179341e+06', '4.067343e+06'] is invalid, the data is
 missing.
 RelaxWarning: The sequence data in the line ['protein', '38', 'E',
 '38', 'N', '1.563795e+06', '2.921316e+06'] is invalid, the data is
 missing.
 RelaxWarning: The sequence data in the line ['protein', '7', 'N', '7',
 'N', '1.535896e+06', '3.005234e+06'] is invalid, the data is missing.
 RelaxWarning: The sequence data in the line ['protein', '75', 'L',
 '75', 'N', '3.578841e+06', '6.352595e+06'] is invalid, the data is
 missing.
 RelaxError: No corresponding data could be found within the file.

 ---

 Troels Emtekær Linnet


 2013/6/6 Edward d'Auvergne edw...@nmr-relax.com:
 Hi,

 Have you had any luck finding the problem?  I would guess that this
 doesn't work as the protein was renamed to something different to that
 of the data file, hence you would see messages such as:

 relax spectrum.read_intensities(file='test.seq', dir=None,
 spectrum_id=None, heteronuc='N', proton='HN', int_method='height',
 int_col=6, spin_id_col=None, mol_name_col=1, res_num_col=2,
 res_name_col=3, spin_num_col=4, spin_name_col=5, int_col=6, sep=None,
 spin_id=None, ncproc=None)
 Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for 
 reading.
 Generic formatted data file.

 RelaxWarning: Cannot find the spin #protein:10@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:6@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:63@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:4@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:67@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:5@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:65@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:38@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:7@N within the sequence.
 RelaxWarning: Cannot find the spin #protein:75@N within the sequence.
 RelaxError: No data could be loaded from the peak list

 I tried this by copying the data in your post to a file and following
 the instructions.  This is normal as the molecule with the name
 'protein' no longer exists in the relax data store.  Or did you see
 something different?  The RelaxError text you wrote about is slightly
 different.

 Regards,

 Edward


 On 4 June 2013 15:10, Edward d'Auvergne edward.dauver...@gmail.com wrote:
 I have to admit, the error message should be made more informative!
 However that error statement (line 668 of lib/io.py) cannot be reached
 without relax giving many warnings.  The only possibility of reaching
 the error without warnings is if the file is empty.  Do you see
 warnings which could indicate the problem?  If not, I would suggest
 creating a bug report for the problem and attaching a minimal set of
 files to be able to reproduce the issue.  It would be best if the
 files are truncated to 1-2 spins (and maybe randomised if the data is
 to be kept secret).  If it really is a bug, then these files could be
 be added to the test suite and turned into a system or GUI test to
 catch the problem.

 Cheers,

 Edward


 On 4 June 2013 14:37, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 I have made a custom intensity peak/model file, for easy import in relax.
 The form is:

 protein 10 L 10 N 3.377659e+05 6.362446e+05
 protein 6 V 6 N 1.697771e+06 3.015788e+06
 protein 63 Y 63 N 8.673898e+05 1.726064e+06
 protein 4 Y 4 N 2.339480e+06 4.039142e+06
 protein 67 M 67 N 2.574062e+06 4.313824e+06
 protein 5 E 5 N 1.609356e+06 2.927111e+06
 protein 65 V 65 N 2.179341e+06 4.067343e+06
 protein 38 E 38 N 1.563795e+06 2.921316e+06
 protein 7 N 7 N 1.535896e+06 3.005234e+06
 protein 75 L 75 N 3.578841e+06 6.352595e+06

 This goes fine for model import, with standard settings.

 Start new analysis
 Relaxation dispersion analysis
 Relaxation dispersion experiment type selection
 CPMG, fixed time
 Data pipe set up
 The starting data pipe for the analysis = origin - relax_disp (Mon Jun
 3 17:08:30 2013)
 The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013)

 Click: Spin editor
 Click: Load spins
 Make a test file: test.seq

 Click: From a file containing sequence data
 The file name = test.seq
 The spin ID string = Leave empty
 Free format
 Molecule name column (mol_name_col) = 1
 Residue number column (res_num_col) = 2
 Residue name column (res_name_col) = 3
 Spin number column (spin_num_col) = 4
 Spin name column (spin_name_col) = 5
 You can then rename molecule

Re: Custom Peak intensity reading

On a different note, if you notice anywhere in relax's execution where
the messages are not informative enough, are misleading, or where
additional messages would be useful, these can all be reported as
bugs. Anything in relax that causes confusion should be considered a
bug which should be fixed.

Regards,

Edward

On 6 June 2013 15:26, Edward d'Auvergne edw...@nmr-relax.com wrote:
Oh, right, I see the problem. This user function currently only has
partial support for simultaneously loading all spectral data at once.
The current way to do this is to change the spectrum ID and intensity
column one-by-one while clicking on 'Apply' as you go. But I have
partly designed this user function to handle this situation, according
to the user function documentation:

Generic intensity file: This is a generic format which can be
created by scripting to support non-supported peak lists. It should
contain in the first few columns enough information to identify the
spin. This can include columns for the molecule name, residue number,
residue name, spin number, and spin name. Alternatively a spin ID
string column can be used. The peak intensities can be placed in
another column specified by the integration column number.
Intensities from multiple spectra can be placed into different
columns, and these can then be specified simultaneously by setting the
integration column value to a list of columns. This list must be
matched by setting the spectrum ID to a list of the same length...

Could you submit a bug report for this, attaching any files required
to replicate the bug? It would be useful to give a link to the Gmane
archive as well (going to
http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on
using frames and threads - finding message - clicking on
[thread] down the botton - and copying the link). I could then
turn the instructions into a relax script, and incorporate both the
script and data files into the test suite directories and create a
system test to catch the bug. Or, if you wish, as a learning exercise
for becoming a relax developer you could give this a go yourself after
creating the report. This would all go into the relax trunk, and then
be ported to the relax_disp branch using svnmerge.py.

Cheers,

Edward

On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote:
I think it is because that:
spectrum_id='(2,6)'

is translated to a string.

Could it be corrected, so it does similar as:
int_col=(6, 7)

Best
Troels Emtekær Linnet

2013/6/6 Troels Emtekær Linnet tlin...@gmail.com:
Hi,

No, not any luck.
And, this time I am not renaming.

Where can I find the longer error message?
-
Add spectra
Click Add

The file name = test.seq
The Spectrum ID string: 2,0
The Intensity column: 6,7

protein 10 L 10 N 3.377659e+05 6.362446e+05
protein 6 V 6 N 1.697771e+06 3.015788e+06
protein 63 Y 63 N 8.673898e+05 1.726064e+06
protein 4 Y 4 N 2.339480e+06 4.039142e+06
protein 67 M 67 N 2.574062e+06 4.313824e+06
protein 5 E 5 N 1.609356e+06 2.927111e+06
protein 65 V 65 N 2.179341e+06 4.067343e+06
protein 38 E 38 N 1.563795e+06 2.921316e+06
protein 7 N 7 N 1.535896e+06 3.005234e+06
protein 75 L 75 N 3.578841e+06 6.352595e+06

--
relax relax_disp.exp_type(exp_type='cpmg fixed')
The fixed relaxation time period CPMG-type experiments.

relax
sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None)
Opening the file
'/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
for reading.
# mol_nameres_numres_namespin_numspin_name
protein 10 L 10 N
protein 6 V 6 N
protein 63 Y 63 N
protein 4 Y 4 N
protein 67 M 67 N
protein 5 E 5 N
protein 65 V 65 N
protein 38 E 38 N
protein 7 N 7 N
protein 75 L 75 N

relax
spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
dir=None, spectrum_id='2,0', heteronuc='N', proton='HN',
int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
sep=None, spin_id=None, ncproc=None)
Opening the file
'/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
for reading.
Generic formatted data file.

RelaxWarning: The sequence data in the line ['protein', '10

Re: Custom Peak intensity reading

This is part of the bug and is the same reason you saw an error in the
GUI.  If you look at the file user_functions/spectrum.py in the relax
trunk source code and go to line 236 (for the current revision
r19893), you should be able to see the issue.

Regards,

Edward


On 6 June 2013 16:44, Troels Emtekær Linnet tlin...@gmail.com wrote:
 In the relax prompt, this can produce the error:

 -
 pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')
 relax_disp.exp_type(exp_type='cpmg fixed')

 sequence.read(file='/sbinlab2/tlinnet/Desktop/test.seq',
 dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
 res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
 spin_id=None)

 spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq',
 dir=None, spectrum_id=(2,0), heteronuc='N', proton='HN',
 int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1,
 res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
 sep=None, spin_id=None, ncproc=None)

   File input, line 3, in module
   File /sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py,
 line 200, in __call__
 lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none)
   File /sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py,
 line 862, in is_str
 raise RelaxStrError(name, arg)
 RelaxStrError:  [31mRelaxError: The spectrum ID string argument '(2,
 0)' must be a string. [0m
 -





 2013/6/6 Edward d'Auvergne edw...@nmr-relax.com:
 On a different note, if you notice anywhere in relax's execution where
 the messages are not informative enough, are misleading, or where
 additional messages would be useful, these can all be reported as
 bugs.  Anything in relax that causes confusion should be considered a
 bug which should be fixed.

 Regards,

 Edward



 On 6 June 2013 15:26, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Oh, right, I see the problem.  This user function currently only has
 partial support for simultaneously loading all spectral data at once.
 The current way to do this is to change the spectrum ID and intensity
 column one-by-one while clicking on 'Apply' as you go.  But I have
 partly designed this user function to handle this situation, according
 to the user function documentation:

 Generic intensity file:  This is a generic format which can be
 created by scripting to support non-supported peak lists.  It should
 contain in the first few columns enough information to identify the
 spin.  This can include columns for the molecule name, residue number,
 residue name, spin number, and spin name.  Alternatively a spin ID
 string column can be used. The peak intensities can be placed in
 another column specified by the integration column number.
 Intensities from multiple spectra can be placed into different
 columns, and these can then be specified simultaneously by setting the
 integration column value to a list of columns.  This list must be
 matched by setting the spectrum ID to a list of the same length...

 Could you submit a bug report for this, attaching any files required
 to replicate the bug?  It would be useful to give a link to the Gmane
 archive as well (going to
 http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on
 using frames and threads - finding message - clicking on 
 [thread]  down the botton - and copying the link).  I could then
 turn the instructions into a relax script, and incorporate both the
 script and data files into the test suite directories and create a
 system test to catch the bug.  Or, if you wish, as a learning exercise
 for becoming a relax developer you could give this a go yourself after
 creating the report.  This would all go into the relax trunk, and then
 be ported to the relax_disp branch using svnmerge.py.

 Cheers,

 Edward



 On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote:
 I think it is because that:
 spectrum_id='(2,6)'

 is translated to a string.

 Could it be corrected, so it does similar as:
 int_col=(6, 7)

 Best
 Troels Emtekær Linnet


 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com:
 Hi,

 No, not any luck.
 And, this time I am not renaming.

 Where can I find the longer error message?
 -
 Add spectra
 Click Add

 The file name = test.seq
 The Spectrum ID string: 2,0
 The Intensity column: 6,7
 
 protein 10 L 10 N 3.377659e+05 6.362446e+05
 protein 6 V 6 N 1.697771e+06 3.015788e+06
 protein 63 Y 63 N 8.673898e+05 1.726064e+06
 protein 4 Y 4 N 2.339480e+06 4.039142e+06
 protein 67 M 67 N 2.574062e+06 4.313824e+06
 protein 5 E 5 N 1.609356e+06 2.927111e+06
 protein 65 V 65 N 2.179341e+06 4.067343e+06
 protein 38 E 38 N 1.563795e+06 2.921316e+06
 protein 7 N 7 N 1.535896e+06 3.005234e+06
 protein 75 L 75 N 3.578841e+06 6.352595e+06
 

 --
 relax relax_disp.exp_type(exp_type='cpmg fixed')
 The fixed relaxation time period CPMG-type experiments.

 relax

Re: Is there a command for opening an auto analysis for a pipe?

Actually this problem is a classical case of bit-rot. The code for
reading peak intensities was written long before Chris MacRaild, Gary
Thompson, and I implemented the relax test suite. So no system, unit,
or GUI tests were ever written for it. Therefore with time, as the
relax code base has been rewritten time after time, this code path has
ceased to function. Luckily bit-rot issues are often very easy to
fix.

There are multiple ways to achieve the same goal in relax, so not all
cases are reported back to the mailing list. Therefore don't be
discouraged if you encounter another such problem. With a detailed
bug report with files attached to demonstrate the issue, I can usually
have a fix for the problem within 5 minutes and a system test written
to prevent the bug from returning.

Regards,

Edward

On 6 June 2013 21:00, Edward d'Auvergne edw...@nmr-relax.com wrote:
I can see that I'm loosing you, so I've created the system test to
catch the bug you see:

http://article.gmane.org/gmane.science.nmr.relax.scm/17668
http://article.gmane.org/gmane.science.nmr.relax.scm/17670
http://article.gmane.org/gmane.science.nmr.relax.scm/17674

I've also fixed the bug:

http://article.gmane.org/gmane.science.nmr.relax.scm/17672
http://article.gmane.org/gmane.science.nmr.relax.scm/17676

This has all been merged into the relax_disp branch using svnmerge.py.
The approach for extracting the user function commands from the log
is correct and will work in all cases.

As for opening the relaxation dispersion tab at start up, this is not
possible. However you can have the same affect by opening a
previously saved state just after you launch relax. If you are
repeating an operation often, then you can save a state just prior to
the repetitive operation and then load that the next time. This saves
a lot of time.

For the number of integration points when performing volume
integration, this is quite important to know for the analysis of the
peak intensity errors. This is not an issue if you have replicated
spectra though, as it is only used to propagate the baseplane RMSD
measurements. Note that this is not implemented in relax yet, but in
the 12 years of relax's existence, no use has asked for this feature
(which is relatively trivial to implement). Also the
spectrum.integration_points page should be skipped in the GUI peak
intensity wizard if you have replicated spectra. I have just fixed
this too:

http://article.gmane.org/gmane.science.nmr.relax.scm/17678

I hope this will allow you to load your data. Most people normally
measure peak heights (I do this in Sparky) and then load the Sparky,
NMRView, or XEasy peak lists one at a time, so these issues have not
been encountered before. Or at least they have never been reported to
the relax mailing lists. These are quite minor though and now should
be fixed. Thank you for creating the bug report
https://gna.org/bugs/?20873, that allowed me to create a system test
and fix these problems, and importantly to make sure they never return
in the future.

Cheers,

Edward

On 6 June 2013 19:57, Troels Emtekær Linnet tlin...@gmail.com wrote:
Hi Edward.

Well, it doesn't solve my problem.
I really just would like to get this program running soon. :-)

I have not been able to run anything until now, and it eats my time...
(But if I can get it to work, then I hopefully can save time).

So, I have made a relax script generator, which defines all the
things relax needs.
But I don't know what it needs, before I run the GUI, and go through the
steps.
Then I parse the necessary information into my script generator, which
makes the
relax script.

So at the moment, I run the gui with the logfile, and try to figure
out, how can I put
that command into my script generator.

And it would be nice, but not necessary, if it could pop up the
Relaxation dispersion tab, when
I open the relax -g.

I think I need one more thing to know.

--
spectrum.integration_points
--
I have used summation over spectrum points with a box of size +/-1
point in dx and dx.
How, can I, should I, then set number of points to 9 ? Or just leave it be?
spectrum.integration_points(N=9, spectrum_id='0_2', spin_id=None)

-
# Create the 'rx' data pipe.
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')

# The type of experiment
relax_disp.exp_type(exp_type='cpmg fixed')

# Read the sequence from file
sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/table_ser_files_model.txt',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None)

# Read the intensities from columns
spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/table_ser_files_model.txt',
dir=None, spectrum_id='0_2', heteronuc

Re: Time of running, Model selection and global/cluster analysis for relaxation dispersion analysis

2013-06-11 Thread Edward d'Auvergne

Hi,

I'll answer below:


 I performed 'cpmg fixed' a  relaxation dispersion analysis, for dataset with
 68 residues.
 Having 22 intensity files, with 4 triple replications.

 I took from 17 pm to 13 pm following day, app 20 hours.
 The analysed models were: R2eff', 'No Rex','LM63','CR72'

 Is 20 hours for an analysis expected?
 , or should I look for some errors somewhere?

This depends.  By default relax uses much higher precision
optimisation than most other softwares.  This is based on the
philosophy that more accurate results are worth the wait, especially
considering that this time is relatively small in comparison to the
measurement and processing time (and adding the inevitable
re-measurements).  In addition, lots of Monte Carlo simulations are
used for really accurately determining your parameter errors.  For
comparison, note that a full a Lipari and Szabo model-free analysis
can take between 1 day and 2 weeks to complete.

For initial analyses where errors are not so important, the number of
simulations can be dropped massively to speed things up.  This can
also be done for students.  The result is that the error estimates of
the parameters are horrible but, in some cases, excluding publication,
that is not such a problem.  This will not affect model selection
either.  Therefore if errors are not important for specific cases,
then set the number of MC sims to 3.  Then watch how much quicker
things run.

Oh, if this is for students using the GUI, you could hack a special
version of relax to have the auto-analysis perform much lower
precision optimisation.  It should be possible to make things run very
quick for them.  If they are using scripting, but still the relaxation
dispersion auto-analysis, then no hacking is necessary.  The function
tolerance and maximum number of iterations can be set using special
tricks ;)


 Relax made a model selection.
 model_selection(method='AIC', modsel_pipe='final', bundle=None, pipes=['No
 Rex', 'LM63', 'CR72'])

 How can I inspect which model is then chosen?

Well, the hard way would be to open the relax saved state in the
'final' directory.  Or to look at the logs.  That information is
unfortunately not presented in a text file.  How would you suggest
that such information is presented?


 Then I would like to make a global fit / cluster analysis.
 Is this implemented yet?

Yes.  You need to use the relax_disp.cluster user function.


 And should I use the:
 User functions (n-z) - relax_disp - cluster ?

I am still thinking about how to bring this into the relaxation
dispersion auto-analysis GUI element without requiring me to write a
lot of code!


 By the way.
 The sherekhan input function is super great!

:)

The CPMGFit and NESSY input user functions will hopefully also be of
use to some people.  However if you start adding some new models to
relax, then relax will soon have all of the capabilities that these
these programs possess.  And if Paul Schanda's numerical integration
Python code is merged into relax, then relax will soon surpass all of
these softwares.


 Thanks a lot :-)
 This is super great

You're welcome.  I'm hoping that you can help to make this even greater ;)

Regards,

Edward

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Re: Time of running, Model selection and global/cluster analysis for relaxation dispersion analysis

2013-06-11 Thread Edward d'Auvergne

If you update your branch, you will now have access to the Ishima and
Torchia 1999 model (labelled as 'IT99').

Regards,

Edward

On 11 June 2013 14:55, Troels Emtekær Linnet tlin...@gmail.com wrote:
 This was the relax commands for the analysis:
 -

 == cpmg fixed ==
 === Initial ===
 pre
 # Create the 'rx' data pipe.
 pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')

 # The type of experiment
 relax_disp.exp_type(exp_type='cpmg fixed')

 # Read the sequence from file
 sequence.read(file='table_ser_files_model.txt',
 dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
 spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)

  Repeat for all peak intensity files
 # Read the intensities from columns
 spectrum.read_intensities(file='table_ser_files_model.txt',
 dir=None, spectrum_id='0_2', heteronuc='N', proton='HN', int_method='point
 sum', int_col=(6), spin_id_col=None, mol_name_col=1,
 res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
 spin_id=None, ncproc=None)

 relax_disp.cpmg_frq(spectrum_id='0_2', cpmg_frq=40.0)
 relax_disp.relax_time(spectrum_id='0_2', time=0.05)
 spectrometer.frequency(id='0_2', frq=750.061, units='MHz')

 #Define replicated:
 relax spectrum.replicated(spectrum_ids=['0_2', '7_2', '14_2'])
 relax spectrum.replicated(spectrum_ids=['15_14', '16_14', '20_14'])
 relax spectrum.replicated(spectrum_ids=['3_30', '8_30', '17_30'])
 relax spectrum.replicated(spectrum_ids=['9_46', '19_46', '22_46'])

 # Define isotope
 relax spin.isotope(isotope='15N', spin_id='@N*', force=True)

 # Make error analysis
 spectrum.error_analysis(subset=['0_2', '1_0', '2_8', '3_30', '4_4', '5_42',
 '6_6', '7_2', '8_30', '9_46', '10_10', '11_18', '12_26', '13_38', '14_2',
 '15_14', '16_14', '17_30', '18_22', '19_46', '20_14', '21_34', '22_46'])
 /pre
 === - The 'R2eff' model - ===
 pre
 pipe.copy(pipe_from='origin rx', pipe_to='R2eff', bundle_to='rx')
 pipe.switch(pipe_name='R2eff')
 relax_disp.select_model(model='R2eff')
 calc(verbosity=1)

 results.write(file='results', dir='R2eff', compress_type=1, force=True)
 relax_disp.plot_disp_curves(dir='R2eff', force=True)
 value.write(param='r2eff', file='r2eff.out', dir='R2eff', scaling=1.0,
 comment=None, bc=False, force=True)
 grace.write(x_data_type='res_num', y_data_type='r2eff', spin_id=None,
 plot_data='value', file='r2eff.agr', dir='R2eff', force=True, norm=False)
 /pre

 === - The 'No Rex' model - ===
 pre
 pipe.copy(pipe_from='origin rx', pipe_to='No Rex', bundle_to='rx')
 pipe.switch(pipe_name='No Rex')
 relax_disp.select_model(model='No Rex')
 value.copy(pipe_from='R2eff', pipe_to='No Rex', param='r2eff')

 grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1)
 minimise(min_algor='simplex', line_search=None, hessian_mod=None,
 hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=1000,
 constraints=True, scaling=True, verbosity=1)

 monte_carlo.setup(number=500)
 monte_carlo.create_data(method='back_calc')
 monte_carlo.initial_values()
 minimise(min_algor='simplex', line_search=None, hessian_mod=None,
 hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=1000,
 constraints=True, scaling=True, verbosity=1)

 monte_carlo.error_analysis()
 results.write(file='results', dir='No Rex', compress_type=1, force=True)
 relax_disp.plot_disp_curves(dir='No Rex', force=True)

 #Value write?

 grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
 plot_data='value', file='chi2.agr', dir='No Rex', force=True, norm=False)
 /pre

 === - The 'LM63' model - ===
 pre
 pipe.copy(pipe_from='origin rx', pipe_to='LM63', bundle_to='rx')
 pipe.switch(pipe_name='LM63')
 relax_disp.select_model(model='LM63')
 value.copy(pipe_from='R2eff', pipe_to='LM63', param='r2eff')

 grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1)
 minimise(min_algor='simplex', line_search=None, hessian_mod=None,
 hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=1000,
 constraints=True, scaling=True, verbosity=1)

 monte_carlo.setup(number=500)
 monte_carlo.create_data(method='back_calc')
 monte_carlo.initial_values()
 minimise(min_algor='simplex', line_search=None, hessian_mod=None,
 hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=1000,
 constraints=True, scaling=True, verbosity=1)

 monte_carlo.error_analysis()
 results.write(file='results', dir='LM63', compress_type=1, force=True)
 relax_disp.plot_disp_curves(dir='LM63', force=True)

 value.write(param='phi_ex', file='phi_ex.out', dir='LM63', scaling=1.0,
 comment=None, bc=False, force=True)
 grace.write(x_data_type='res_num', y_data_type='phi_ex', spin_id=None,
 plot_data='value', file='phi_ex.agr', dir='LM63', force=True, norm=False)

 grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
 plot_data='value', file='chi2.agr', dir='LM63', force=True, norm=False)
 /pre

 === - The 'CR72' model - ===
 pre

Re: A tip for converting the result directories xmgrace files to eps and png

That's a great trick!  My knowledge of Grace is not that extensive.
You know what would be even better - if the
relax_disp.plot_disp_curves user function created this script and
dropped it into the directory with the Grace files!  I've now shifted
the code into the
specific_analyses.relax_disp.disp_data.plot_disp_curves() function.
Such a script could easily be created at the end of this function -
best by calling a special function in lib.software.grace.

What would be good would be to generate one script for the PNG files,
maybe called 'grace_to_png.sh' just to be more informative to the user
that this is for conversion and that it is a shell script, one for EPS
files called possibly 'grace_to_eps.sh', and a third called
'eps_to_pdf.sh'.  The plot_disp_curves() function can even make them
executable for the user.  I suggest that the *.tmp files be removed by
the script at the end.

The only problem is that I tried this and received error messages and
broken files:

Unknown device: DEVICE PNG FONT ANTIALIASING ON
Unknown device: DEVICE PNG OP compression:9
File modifications are disabled in safe mode: PRINT
File modifications are disabled in safe mode: PRINT
disp_:70@N agr

The EPS files are created successfully.  I'm not sure why the PNGs
failed, maybe it's not compiled in.  JPEG and SVG are present in the
print options through the GUI though, so maybe scripts for these
formats can be very easily created as well.  A simple loop over 'PNG',
'EPS', 'SVG', and 'JPEG' could create separate scripts for each format
and make them executable, and then at the end the 'eps_to_pdf.sh' can
be created.  The script generation could be documented in the user
function docstring.  What do you think?

Cheers,

Edward


On 13 June 2013 14:31, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 I got tired of opening each xmgrace file to see the plot.
 I found that to export to png, you need to:

 Add this to the end of the xmgrace file

 #Print out to
 @PRINT TO /home/you/output.png
 @HARDCOPY DEVICE PNG
 @DEVICE PNG FONT ANTIALIASING on
 # Make white background transparent
 #@DEVICE PNG OP transparent:on
 @DEVICE PNG OP compression:9
 @PRINT

 Then issue an HARDCOPY with xmgrace
 xmgrace -hardcopy xmgracefile.agr


 Script to make both png and eps for a folder with xmgrace files

 Write in: xmgrace_png
 and put in your bin folder

 #!/bin/bash

 for gracefile in *.agr; do
 filename=$(basename $gracefile)
 extension=${filename##*.}
 filename=${filename%.*}

 TMPPNG=${filename}_png.tmp
 cat $gracefile  $TMPPNG
 echo #Print out to  $TMPPNG
 echo '@PRINT TO '${PWD}/${filename}.png''  $TMPPNG
 echo '@HARDCOPY DEVICE PNG'  $TMPPNG
 echo '@DEVICE PNG FONT ANTIALIASING on'  $TMPPNG
 echo '# Make white background transparent'  $TMPPNG
 echo '#@DEVICE PNG OP transparent:on'  $TMPPNG
 echo '@DEVICE PNG OP compression:9'  $TMPPNG
 echo '@PRINT'  $TMPPNG
 xmgrace -hardcopy $TMPPNG

 TMPEPS=${filename}_eps.tmp
 cat $gracefile  $TMPEPS
 echo #Print out to  $TMPEPS
 echo '@PRINT TO '${PWD}/${filename}.eps''  $TMPEPS
 echo '@HARDCOPY DEVICE EPS'  $TMPEPS
 echo '@DEVICE EPS OP level2'  $TMPEPS
 echo '@PRINT'  $TMPEPS
 xmgrace -hardcopy $TMPEPS

 echo $filename $extension
 #eps2png -resolution 200 $TMPEPS
 #epstopdf $TMPEPS
 done

 Then just make chmod +x xmgrace_png
 and in the folder, issue an:

 xmgrace_png

 sit back and relax

 If you want to convert eps to pdf

 bash ;
 for epsfile in *.eps; epstopdf $epsfile; echo Making pdf: $epsfile; done

 Troels Emtekær Linnet

 ___
 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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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: A tip for converting the result directories xmgrace files to eps and png

Would you like to try to give this a go?

Regards,

Edward


On 13 June 2013 16:35, Troels Emtekær Linnet tlin...@gmail.com wrote:
 I am happy that you think it is great. :-)

 As soon there is a file type, which can fast be opened by a image viewer, I
 am happy.

 It works for PNG here, and it is very probably a compilation issue.
 I have PNG as a possibility to print in my xmgrace menu.

 I found the commands here:
 http://ringo.ams.sunysb.edu/index.php/Xmgrace

 This is for EPS and PNG, but I havent found options for JPEG yet.

 I would say the more the merrier.
 It take's time to create scripts, but no time to delete.

 Best
 Troels




 Troels Emtekær Linnet


 2013/6/13 Edward d'Auvergne edw...@nmr-relax.com

 That's a great trick!  My knowledge of Grace is not that extensive.
 You know what would be even better - if the
 relax_disp.plot_disp_curves user function created this script and
 dropped it into the directory with the Grace files!  I've now shifted
 the code into the
 specific_analyses.relax_disp.disp_data.plot_disp_curves() function.
 Such a script could easily be created at the end of this function -
 best by calling a special function in lib.software.grace.

 What would be good would be to generate one script for the PNG files,
 maybe called 'grace_to_png.sh' just to be more informative to the user
 that this is for conversion and that it is a shell script, one for EPS
 files called possibly 'grace_to_eps.sh', and a third called
 'eps_to_pdf.sh'.  The plot_disp_curves() function can even make them
 executable for the user.  I suggest that the *.tmp files be removed by
 the script at the end.

 The only problem is that I tried this and received error messages and
 broken files:

 Unknown device: DEVICE PNG FONT ANTIALIASING ON
 Unknown device: DEVICE PNG OP compression:9
 File modifications are disabled in safe mode: PRINT
 File modifications are disabled in safe mode: PRINT
 disp_:70@N agr

 The EPS files are created successfully.  I'm not sure why the PNGs
 failed, maybe it's not compiled in.  JPEG and SVG are present in the
 print options through the GUI though, so maybe scripts for these
 formats can be very easily created as well.  A simple loop over 'PNG',
 'EPS', 'SVG', and 'JPEG' could create separate scripts for each format
 and make them executable, and then at the end the 'eps_to_pdf.sh' can
 be created.  The script generation could be documented in the user
 function docstring.  What do you think?

 Cheers,

 Edward


 On 13 June 2013 14:31, Troels Emtekær Linnet tlin...@gmail.com wrote:
  Hi.
 
  I got tired of opening each xmgrace file to see the plot.
  I found that to export to png, you need to:
 
  Add this to the end of the xmgrace file
 
  #Print out to
  @PRINT TO /home/you/output.png
  @HARDCOPY DEVICE PNG
  @DEVICE PNG FONT ANTIALIASING on
  # Make white background transparent
  #@DEVICE PNG OP transparent:on
  @DEVICE PNG OP compression:9
  @PRINT
 
  Then issue an HARDCOPY with xmgrace
  xmgrace -hardcopy xmgracefile.agr
 
 
  Script to make both png and eps for a folder with xmgrace files
 
  Write in: xmgrace_png
  and put in your bin folder
 
  #!/bin/bash
 
  for gracefile in *.agr; do
  filename=$(basename $gracefile)
  extension=${filename##*.}
  filename=${filename%.*}
 
  TMPPNG=${filename}_png.tmp
  cat $gracefile  $TMPPNG
  echo #Print out to  $TMPPNG
  echo '@PRINT TO '${PWD}/${filename}.png''  $TMPPNG
  echo '@HARDCOPY DEVICE PNG'  $TMPPNG
  echo '@DEVICE PNG FONT ANTIALIASING on'  $TMPPNG
  echo '# Make white background transparent'  $TMPPNG
  echo '#@DEVICE PNG OP transparent:on'  $TMPPNG
  echo '@DEVICE PNG OP compression:9'  $TMPPNG
  echo '@PRINT'  $TMPPNG
  xmgrace -hardcopy $TMPPNG
 
  TMPEPS=${filename}_eps.tmp
  cat $gracefile  $TMPEPS
  echo #Print out to  $TMPEPS
  echo '@PRINT TO '${PWD}/${filename}.eps''  $TMPEPS
  echo '@HARDCOPY DEVICE EPS'  $TMPEPS
  echo '@DEVICE EPS OP level2'  $TMPEPS
  echo '@PRINT'  $TMPEPS
  xmgrace -hardcopy $TMPEPS
 
  echo $filename $extension
  #eps2png -resolution 200 $TMPEPS
  #epstopdf $TMPEPS
  done
 
  Then just make chmod +x xmgrace_png
  and in the folder, issue an:
 
  xmgrace_png
 
  sit back and relax
 
  If you want to convert eps to pdf
 
  bash ;
  for epsfile in *.eps; epstopdf $epsfile; echo Making pdf: $epsfile;
  done
 
  Troels Emtekær Linnet
 
  ___
  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

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: A tip for converting the result directories xmgrace files to eps and png

Great!  For the 64-bit issue, if you look in the file for that test
you might be able to see what I am doing with this.  The file to look
at and the line to go to is given at the end of the traceback message
which you attached to the bug report (https://gna.org/bugs/?20821).
For a hint, the problem has something to do with precision variability
between different setups.  As for adding new models, this is pretty
straight forward when following the tutorial at:

http://thread.gmane.org/gmane.science.nmr.relax.devel/3907

From my commit messages, you can probably see that it only take me a
few hours per dispersion model.  Note that I have now copied this
tutorial, as well as the docstring for the relax_disp.select_model
user function and created a basic initial relaxation dispersion
chapter in the relax manual.  If you know LaTeX then, when adding the
model, it would good to add the equations and reference via a bibtex
entry to that chapter.  If you have Scons and LaTeX installed on your
system, the manual can be built by typing:

$ scons user_manual_pdf

Cheers,

Edward



On 13 June 2013 17:25, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Sure why not :-)

 And I am soon in the mood for the Tollinger/Kay equation.
 And solve the 64 bit problem in windows.

 Can you guide me in the direction where I should look for the 64 bit
 problem?

 Best
 troels

 Troels Emtekær Linnet


 2013/6/13 Edward d'Auvergne edw...@nmr-relax.com

 Would you like to try to give this a go?

 Regards,

 Edward


 On 13 June 2013 16:35, Troels Emtekær Linnet tlin...@gmail.com wrote:
  I am happy that you think it is great. :-)
 
  As soon there is a file type, which can fast be opened by a image
  viewer, I
  am happy.
 
  It works for PNG here, and it is very probably a compilation issue.
  I have PNG as a possibility to print in my xmgrace menu.
 
  I found the commands here:
  http://ringo.ams.sunysb.edu/index.php/Xmgrace
 
  This is for EPS and PNG, but I havent found options for JPEG yet.
 
  I would say the more the merrier.
  It take's time to create scripts, but no time to delete.
 
  Best
  Troels
 
 
 
 
  Troels Emtekær Linnet
 
 
  2013/6/13 Edward d'Auvergne edw...@nmr-relax.com
 
  That's a great trick!  My knowledge of Grace is not that extensive.
  You know what would be even better - if the
  relax_disp.plot_disp_curves user function created this script and
  dropped it into the directory with the Grace files!  I've now shifted
  the code into the
  specific_analyses.relax_disp.disp_data.plot_disp_curves() function.
  Such a script could easily be created at the end of this function -
  best by calling a special function in lib.software.grace.
 
  What would be good would be to generate one script for the PNG files,
  maybe called 'grace_to_png.sh' just to be more informative to the user
  that this is for conversion and that it is a shell script, one for EPS
  files called possibly 'grace_to_eps.sh', and a third called
  'eps_to_pdf.sh'.  The plot_disp_curves() function can even make them
  executable for the user.  I suggest that the *.tmp files be removed by
  the script at the end.
 
  The only problem is that I tried this and received error messages and
  broken files:
 
  Unknown device: DEVICE PNG FONT ANTIALIASING ON
  Unknown device: DEVICE PNG OP compression:9
  File modifications are disabled in safe mode: PRINT
  File modifications are disabled in safe mode: PRINT
  disp_:70@N agr
 
  The EPS files are created successfully.  I'm not sure why the PNGs
  failed, maybe it's not compiled in.  JPEG and SVG are present in the
  print options through the GUI though, so maybe scripts for these
  formats can be very easily created as well.  A simple loop over 'PNG',
  'EPS', 'SVG', and 'JPEG' could create separate scripts for each format
  and make them executable, and then at the end the 'eps_to_pdf.sh' can
  be created.  The script generation could be documented in the user
  function docstring.  What do you think?
 
  Cheers,
 
  Edward
 
 
  On 13 June 2013 14:31, Troels Emtekær Linnet tlin...@gmail.com wrote:
   Hi.
  
   I got tired of opening each xmgrace file to see the plot.
   I found that to export to png, you need to:
  
   Add this to the end of the xmgrace file
  
   #Print out to
   @PRINT TO /home/you/output.png
   @HARDCOPY DEVICE PNG
   @DEVICE PNG FONT ANTIALIASING on
   # Make white background transparent
   #@DEVICE PNG OP transparent:on
   @DEVICE PNG OP compression:9
   @PRINT
  
   Then issue an HARDCOPY with xmgrace
   xmgrace -hardcopy xmgracefile.agr
  
  
   Script to make both png and eps for a folder with xmgrace files
  
   Write in: xmgrace_png
   and put in your bin folder
  
   #!/bin/bash
  
   for gracefile in *.agr; do
   filename=$(basename $gracefile)
   extension=${filename##*.}
   filename=${filename%.*}
  
   TMPPNG=${filename}_png.tmp
   cat $gracefile  $TMPPNG
   echo #Print out to  $TMPPNG
   echo '@PRINT TO '${PWD}/${filename}.png''  $TMPPNG
   echo '@HARDCOPY

Re: Time of running, Model selection and global/cluster analysis for relaxation dispersion analysis