Also, Congrats to Edward!
On Thu, Sep 29, 2016 at 4:11 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
wrote:
> Hi Troels,
>
> I will upload a bug report with the pdb file, the script I use, and the
> data I'm using.
>
> Sincerely,
> Sam
>
> On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Hm...
>>
>> I had a look in: pipe_control/minimise.py
>>
>> The trouble start with line
>> "elif values[i] in [None, {}, []]:"
>>
>> Where the index "i" is running out of bounds.
>>
>> The index is drawn from range(n).
>> n = len(names)
>> names = api.get_param_names(model_info)
>> values = api.get_param_values(model_info)
>>
>> So "something" is not aligned well in the data structures.
>> It seems that the index of parameter names exceeds parameter values.
>>
>>
>> One guess is, that the selection of
>> * diff_model
>> * mf_models
>> * local_tm_models
>>
>> is not correctly set. But I reach my limit of being able to help you.
>> Edward is the expert here, but he is on paternity leave.
>>
>>
>> Another possibility is that some of the spins are in "select" mode, where
>> they maybe should be in "deselect" mode.
>>
>> Maybe the spins do not carry any data from before, and somehow relax
>> expect this.
>>
>> It's very tricky to figure out!
>>
>> A bug report, some minimum data, and a script which make the bug occur
>> can solve this.
>>
>> Then I can write a systemtest, if it relax which is failing.
>>
>> Best
>> Troels
>>
>>
>>
>>
>> 2016-09-29 0:23 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>
>>> 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/explor
>>> e/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 <module>
>>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA
>>> L_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?
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>> 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]>
>>>>
>>>>
>>>> On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>>> wrote:
>>>>
>>>>> Hi Troels,
>>>>>
>>>>> An update on protein number 1: I have successfully resolved the
>>>>> problem. Initially the pdb file had HN instead of just H for the backbone
>>>>> hydrogens. So it couldn't read it. I changed all the HN to H. Then I
>>>>> recieved the error
>>>>> RelaxError: Multiple alternate location indicators are present in the
>>>>> PDB file, but the desired coordinate set has not been specified
>>>>> By removing the extra N, all the text for the 3D location (the
>>>>> co-ordinates) for the HN were shifted a space (no longer aligned). Once I
>>>>> aligned them all, relax was able to read all the spins. So its working
>>>>> now.
>>>>> I'm currently running the test suite as well.
>>>>>
>>>>> Sincerely,
>>>>> Sam
>>>>>
>>>>> On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet <
>>>>> tlin...@nmr-relax.com> wrote:
>>>>>
>>>>>> To test the speed difference between script and GUI,
>>>>>> you could try to run the full test-suite through the terminal or
>>>>>> inside the GUI.
>>>>>>
>>>>>> That should give you a clue about time difference.
>>>>>>
>>>>>>
>>>>>> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet <
>>>>>> tlin...@nmr-relax.com>:
>>>>>>
>>>>>>> If you get different results, for the same setup, this is not good.
>>>>>>> Not at all !
>>>>>>>
>>>>>>> Have you run the full relax test suite after installation?
>>>>>>>
>>>>>>> http://wiki.nmr-relax.com/Installation_test
>>>>>>>
>>>>>>> run it with:
>>>>>>> relax -x
>>>>>>>
>>>>>>> This takes about 1 Hour to run, and should not be used with multiple
>>>>>>> processors.
>>>>>>>
>>>>>>> Relax will test itself with thousands of unit tests and system
>>>>>>> tests, and confer that all
>>>>>>> results are the same.
>>>>>>>
>>>>>>> If the system tests do not pass on each system, something fishy is
>>>>>>> going on.
>>>>>>>
>>>>>>> This is the best line of defence against "systems" acting weird due
>>>>>>> to software/packages etc. etc.
>>>>>>>
>>>>>>> Best
>>>>>>> Troels
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>
>>>>>>>> Hi Troels,
>>>>>>>>
>>>>>>>> I wanted to give a bit of feedback on the results I've obtained
>>>>>>>> throughout the few weeks I've been using model free on relax. First
>>>>>>>> off,
>>>>>>>> thank you guys (both you and Edward) immensly for your patience and
>>>>>>>> help as
>>>>>>>> I attempted to understand and work relax. Secondly, I have noticed a
>>>>>>>> difference between using the gui and the terminal (using scripts to run
>>>>>>>> relax). I've currently finished about 3 runs using the gui, and 3 runs
>>>>>>>> using the terminal (all the same data sets, same pdb files, same
>>>>>>>> settings,
>>>>>>>> etc.). The gui takes about a week to finish, where the terminal takes
>>>>>>>> approximately 24 hours. I've tried this on 2 proteins, both had the
>>>>>>>> same
>>>>>>>> results. The terminal is by far, much faster than the gui. Finally,
>>>>>>>> I've
>>>>>>>> run 1 protein on 2 different computers (one using the multi-processor
>>>>>>>> platform, and on another computer, single-processor). The data sets
>>>>>>>> were
>>>>>>>> all the same, the same pdb file, etc. , but the results I obtained
>>>>>>>> from the
>>>>>>>> computers were slightly different. For the most part, most of the
>>>>>>>> difference in the data was similar, slightly different, but within the
>>>>>>>> error. But there were about 7 or 8 data points that appeared in one
>>>>>>>> run on
>>>>>>>> one computer, and were absent in another run on another computer. This
>>>>>>>> happened in both the S^2 I analyzed and the Rex.
>>>>>>>> I.e. On the fedora 20 (single processor), say I had S^2 values for
>>>>>>>> amino acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On
>>>>>>>> the
>>>>>>>> fedora 24 (multi-processor), I might be missing a value for amino acid
>>>>>>>> 24,
>>>>>>>> but I would have S^2 values for 28,29 and 30. Note the data sets are
>>>>>>>> all
>>>>>>>> the same, the pdb files the same, settings the same, I used the same
>>>>>>>> script
>>>>>>>> for both. The only difference between these runs is they were run on
>>>>>>>> different computer and one was single processor well another was multi.
>>>>>>>> I don't know why I obtained different data from 2 different runs,
>>>>>>>> when the input was all the same, just on different computers.
>>>>>>>> However the S^2 values do make sense. The Rex values were
>>>>>>>> incredibly small (1x10^-20), but there are some similarities (in terms
>>>>>>>> of
>>>>>>>> big Rex values) between the Rex I obtained from relax, and CPMG data
>>>>>>>> analyzed by glove. So I have been able to obtain some reasonable data
>>>>>>>> and
>>>>>>>> results from model_free using relax.
>>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>> Sam
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam <
>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi Troels,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I have attempted the fix for running on a multi-processor platform
>>>>>>>>> by creating the script you told me too, and I still got the same
>>>>>>>>> result. I
>>>>>>>>> have uploaded a screenshot that shows again, relax is running in the
>>>>>>>>> background, but there is no output for relax, nor can I input any
>>>>>>>>> commands.
>>>>>>>>> The only output I recieve is this:
>>>>>>>>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>>>>>>>>
>>>>>>>>> And any command I type in after that gets no response.
>>>>>>>>>
>>>>>>>>> I've also checked the spins via script. For 2 scenarios. Scenario
>>>>>>>>> 1- All hydrogens are kept as HN and Scenario 2- I change all the HN
>>>>>>>>> spins
>>>>>>>>> to H.
>>>>>>>>> The output from Scenario one is, it read all the Nitrogen spins
>>>>>>>>> accordingly :
>>>>>>>>> Objects:
>>>>>>>>> element: 'N'
>>>>>>>>> isotope: '15N'
>>>>>>>>> name: 'N'
>>>>>>>>> num: 1304
>>>>>>>>> pos: array([ 13.196999999999999, 15.218 ,
>>>>>>>>> 3.192 ])
>>>>>>>>> select: True
>>>>>>>>> hRGS4 178 THR #hRGS4:178@1304
>>>>>>>>> Class containing all the spin system specific data.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Objects:
>>>>>>>>> element: 'N'
>>>>>>>>> isotope: '15N'
>>>>>>>>> name: 'N'
>>>>>>>>> num: 2617
>>>>>>>>> pos: array([ 22.696000000000002, 10.683999999999999,
>>>>>>>>> -4.15 ])
>>>>>>>>> select: True
>>>>>>>>> hRGS4 178 THR #hRGS4:178@2617
>>>>>>>>>
>>>>>>>>> But no hydrogens.
>>>>>>>>>
>>>>>>>>> Scenario 2- I still recieve the same error.
>>>>>>>>> RelaxError: Multiple alternate location indicators are present in
>>>>>>>>> the PDB file, but the desired coordinate set has not been specified.
>>>>>>>>>
>>>>>>>>> Sincerely,
>>>>>>>>> Sam
>>>>>>>>>
>>>>>>>>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <
>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Troels,
>>>>>>>>>>
>>>>>>>>>> I have attempted the fix for running on a multi-processor
>>>>>>>>>> platform by creating the script you told me too, and I still got the
>>>>>>>>>> same
>>>>>>>>>> result. I have uploaded a screenshot that shows again, relax is
>>>>>>>>>> running in
>>>>>>>>>> the background, but there is no output for relax, nor can I input any
>>>>>>>>>> commands. The only output I recieve is this:
>>>>>>>>>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>>>>>>>>>
>>>>>>>>>> And any command I type in after that gets no response.
>>>>>>>>>>
>>>>>>>>>> Sincerely,
>>>>>>>>>> Sam
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet <
>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>
>>>>>>>>>>> Try to load the pdb file and make a spin_loop over the
>>>>>>>>>>> information.
>>>>>>>>>>> How does the information look like?
>>>>>>>>>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_s
>>>>>>>>>>> am_mahdi#Check_the_spin_containers_via_script
>>>>>>>>>>>
>>>>>>>>>>> Regarding the multiprocessor on your Fedora 20 machine, try to
>>>>>>>>>>> have a look at the bug.
>>>>>>>>>>> https://gna.org/bugs/?25084
>>>>>>>>>>>
>>>>>>>>>>> -----
>>>>>>>>>>> I suspect there is a mismatch between two installations of
>>>>>>>>>>> relax.
>>>>>>>>>>> One version of 2.x and one local of 4.x.
>>>>>>>>>>> Try adding the full path to relax
>>>>>>>>>>> -----
>>>>>>>>>>>
>>>>>>>>>>> Try make a run script like this and copy it some where to your
>>>>>>>>>>> PATH
>>>>>>>>>>> myrelax
>>>>>>>>>>> ------
>>>>>>>>>>>
>>>>>>>>>>> #!/bin/tcsh -fe
>>>>>>>>>>>
>>>>>>>>>>> # Set the relax version used for this script.
>>>>>>>>>>> set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # Set number of available CPUs.
>>>>>>>>>>> set NPROC=`nproc`
>>>>>>>>>>> set NP=`echo $NPROC + 0 | bc `
>>>>>>>>>>> echo "Running relax with NP=$NP in multi-processor mode"
>>>>>>>>>>>
>>>>>>>>>>> # Run relax in multi processor mode.
>>>>>>>>>>> mpirun -np $NP $RELAX --multi='mpi4py' $argv
>>>>>>>>>>>
>>>>>>>>>>> 2016-09-24 1:03 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>>>>>>>>>> :
>>>>>>>>>>>
>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>
>>>>>>>>>>>> Update on Protein number 1: So I was able to successfully run
>>>>>>>>>>>> model free with no problems on my protein (I don't know why it was
>>>>>>>>>>>> giving
>>>>>>>>>>>> problems before). The reason it may have been giving issues though
>>>>>>>>>>>> is the
>>>>>>>>>>>> protein I am working with forms a dimer at the concentrations we
>>>>>>>>>>>> work with
>>>>>>>>>>>> (thus the results I have are for the Dimer form of the protein).
>>>>>>>>>>>> The pdb
>>>>>>>>>>>> file though only has a monomer structure though. I have been able
>>>>>>>>>>>> to obtain
>>>>>>>>>>>> the dimer pdb file using HADDOCK (docking program), but have come
>>>>>>>>>>>> across a
>>>>>>>>>>>> few problems uploading the pdb file.
>>>>>>>>>>>> The initial problem was that all the hydrogens attached to the
>>>>>>>>>>>> nitrogen were HN labeled on the HADDOCK modified pdb file, and
>>>>>>>>>>>> model free
>>>>>>>>>>>> could not understand what HN meant, and I would recieve this
>>>>>>>>>>>> warning.
>>>>>>>>>>>> RelaxWarning: Cannot determine the element associated with atom
>>>>>>>>>>>> 'HN'.
>>>>>>>>>>>>
>>>>>>>>>>>> I could however load up all the Nitrogen, but naturally, with
>>>>>>>>>>>> no hydrogens, it wouldn't be able to calculate any bond vectors
>>>>>>>>>>>> between
>>>>>>>>>>>> nitrogen and hydrogen. So I would recieve this error and the
>>>>>>>>>>>> program would
>>>>>>>>>>>> close
>>>>>>>>>>>> RelaxError: The spin ID '@H' matches no spins.
>>>>>>>>>>>>
>>>>>>>>>>>> To fix this, I changed all the HN spins, to just H, but then
>>>>>>>>>>>> recieved another error.
>>>>>>>>>>>> RelaxError: Multiple alternate location indicators are present
>>>>>>>>>>>> in the PDB file, but the desired coordinates set has not been
>>>>>>>>>>>> specified.
>>>>>>>>>>>>
>>>>>>>>>>>> I don't exactly understand what this error means. Is it saying
>>>>>>>>>>>> the program can't locate the 3D coordinates for the Hydrogen and
>>>>>>>>>>>> Nitrogen?
>>>>>>>>>>>> If that is the case, why was it able to before, when it couldn't
>>>>>>>>>>>> read any
>>>>>>>>>>>> of the Hydrogen spins. I'm just confused a bit as to what this
>>>>>>>>>>>> error means.
>>>>>>>>>>>>
>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>> Sam
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam <
>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Update on protein number 1. I ran it with only 5 simulations.
>>>>>>>>>>>>> It took a while, but it ended up finishing. So I assume its due
>>>>>>>>>>>>> to bad data
>>>>>>>>>>>>> simply slowing down the process.
>>>>>>>>>>>>> Update on protein number 2. I ran it with only 2 spins as
>>>>>>>>>>>>> well, and I still recieved the same error. I suspect its due to
>>>>>>>>>>>>> the pdb
>>>>>>>>>>>>> file. I'm going to attempt to use another program to add the
>>>>>>>>>>>>> hydrogens to
>>>>>>>>>>>>> my pdb file and try again.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam <
>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thats weird, I can open it up directly from the link you sent
>>>>>>>>>>>>>> me. I'll reupload it
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet <
>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The file:
>>>>>>>>>>>>>>> file #28673: relax -i data for 4.0,2 a
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> https://gna.org/bugs/download.php?file_id=28673
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Its emtpy?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 2016-09-20 20:05 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I am a bit confused what you are talking about. There is no
>>>>>>>>>>>>>>>> file labeled .?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On
>>>>>>>>>>>>>>>>> https://gna.org/bugs/?25084
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I cannot open the file.?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> In the meantime, try to specify the full path to relax.
>>>>>>>>>>>>>>>>> Not just ./relax
>>>>>>>>>>>>>>>>> but /home/user/xxx/relax
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I just uploaded the 4.0.2 relax -i info. I already have
>>>>>>>>>>>>>>>>>> minfx 1.0.12 with 4.0.2. But I can't open relax on multi
>>>>>>>>>>>>>>>>>> processor
>>>>>>>>>>>>>>>>>> platform for either version.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
>>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Please upgrade!
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Name Installed Version Current
>>>>>>>>>>>>>>>>>>> version
>>>>>>>>>>>>>>>>>>> minfx True 1.0.4
>>>>>>>>>>>>>>>>>>> 1.0.12
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> relax information:
>>>>>>>>>>>>>>>>>>> Version: 2.2.5
>>>>>>>>>>>>>>>>>>> 4.0.2
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I have uploaded the bug report for the issue with
>>>>>>>>>>>>>>>>>>>> running relax on multiple processors on my fedora 20
>>>>>>>>>>>>>>>>>>>> computer. I will
>>>>>>>>>>>>>>>>>>>> upload the mpirun report bindings on the fedora 24
>>>>>>>>>>>>>>>>>>>> computer later today
>>>>>>>>>>>>>>>>>>>> (that is not my lab so I don't have access to it, and the
>>>>>>>>>>>>>>>>>>>> professor is not
>>>>>>>>>>>>>>>>>>>> in yet). If there is any more info that is needed please
>>>>>>>>>>>>>>>>>>>> let me know.
>>>>>>>>>>>>>>>>>>>> Thanks again in advance.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks for the quick response!
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Protein 1: I will attempt to troubleshoot using the
>>>>>>>>>>>>>>>>>>>>> advice you gave me. The problem occurs write after it
>>>>>>>>>>>>>>>>>>>>> indicates its writing
>>>>>>>>>>>>>>>>>>>>> a file for prolate round_3 (so its about to start it). I
>>>>>>>>>>>>>>>>>>>>> will run it again
>>>>>>>>>>>>>>>>>>>>> and post the output to give you a better idea. I'm pretty
>>>>>>>>>>>>>>>>>>>>> sure the output
>>>>>>>>>>>>>>>>>>>>> was something like this
>>>>>>>>>>>>>>>>>>>>> Over-fit spin deselection:
>>>>>>>>>>>>>>>>>>>>> No spins have been deselected.
>>>>>>>>>>>>>>>>>>>>> Resetting the minimisation statistics.
>>>>>>>>>>>>>>>>>>>>> But I will double check and send you another email
>>>>>>>>>>>>>>>>>>>>> with the actual output.
>>>>>>>>>>>>>>>>>>>>> Protein 2:
>>>>>>>>>>>>>>>>>>>>> I am using the sample script for dAuvergene protocol.
>>>>>>>>>>>>>>>>>>>>> So the only thing I've changed since my previous run (the
>>>>>>>>>>>>>>>>>>>>> one that worked
>>>>>>>>>>>>>>>>>>>>> that you wrote a tutorial for), was the pdb file and the
>>>>>>>>>>>>>>>>>>>>> data set I used.
>>>>>>>>>>>>>>>>>>>>> The thing I suspected was causing an issue ,was the pdb
>>>>>>>>>>>>>>>>>>>>> file since I
>>>>>>>>>>>>>>>>>>>>> slightly modified it, and thats really the only thing
>>>>>>>>>>>>>>>>>>>>> different from this
>>>>>>>>>>>>>>>>>>>>> run versus the others.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Also side note, if I were to deselect the spins that I
>>>>>>>>>>>>>>>>>>>>> don't have data for or I have bad data for, that wouldn't
>>>>>>>>>>>>>>>>>>>>> change any of the
>>>>>>>>>>>>>>>>>>>>> calculations correct? I never have since I assumed relax
>>>>>>>>>>>>>>>>>>>>> would just ignore
>>>>>>>>>>>>>>>>>>>>> all the amino acids I don't have data for, but it may
>>>>>>>>>>>>>>>>>>>>> help increase the
>>>>>>>>>>>>>>>>>>>>> speed of my calculations if I just tell relax to just
>>>>>>>>>>>>>>>>>>>>> ignore the spins from
>>>>>>>>>>>>>>>>>>>>> the start.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet
>>>>>>>>>>>>>>>>>>>>> <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Happy to hear you that you get some progress.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Protein 1:
>>>>>>>>>>>>>>>>>>>>>> Can you help me to find out, if you are minimizing or
>>>>>>>>>>>>>>>>>>>>>> running Monte-Carlo simulations?
>>>>>>>>>>>>>>>>>>>>>> This COULD be the problem:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> How relax works (at least how it works for relaxation
>>>>>>>>>>>>>>>>>>>>>> dispersion):
>>>>>>>>>>>>>>>>>>>>>> Step 1: Minimize the error for the target function.
>>>>>>>>>>>>>>>>>>>>>> Find the parameters which best match the target function
>>>>>>>>>>>>>>>>>>>>>> to the data, by
>>>>>>>>>>>>>>>>>>>>>> minimizing the error.
>>>>>>>>>>>>>>>>>>>>>> Here each individual spin minimization is handed out
>>>>>>>>>>>>>>>>>>>>>> to a processor for calculation.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Step 2: Determine the error of the minimization by
>>>>>>>>>>>>>>>>>>>>>> monte carlo simulations.
>>>>>>>>>>>>>>>>>>>>>> Create (Standard 500) additional datasets with a copy
>>>>>>>>>>>>>>>>>>>>>> from the original. Modify each datapoint by an error,
>>>>>>>>>>>>>>>>>>>>>> drawn from a gaussian
>>>>>>>>>>>>>>>>>>>>>> distribution where the width is described by the error
>>>>>>>>>>>>>>>>>>>>>> of measurements.
>>>>>>>>>>>>>>>>>>>>>> Now hand out each of the datasets to the processor.
>>>>>>>>>>>>>>>>>>>>>> Each processor should now calculate the minimization for
>>>>>>>>>>>>>>>>>>>>>> all the spins. The
>>>>>>>>>>>>>>>>>>>>>> minimization should be more quick, as the starting
>>>>>>>>>>>>>>>>>>>>>> position is chosen from
>>>>>>>>>>>>>>>>>>>>>> Step 1.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Possible problem: One (or more) of the spins has
>>>>>>>>>>>>>>>>>>>>>> really bad data. So a little change of the data makes
>>>>>>>>>>>>>>>>>>>>>> the minimization
>>>>>>>>>>>>>>>>>>>>>> space very different.
>>>>>>>>>>>>>>>>>>>>>> Think of a flat table. Where should the "minimization
>>>>>>>>>>>>>>>>>>>>>> ball" run into? Maybe you have created a small new bump
>>>>>>>>>>>>>>>>>>>>>> in the table. This
>>>>>>>>>>>>>>>>>>>>>> is typically for "bad" data.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> This could either be the measurement OR the error
>>>>>>>>>>>>>>>>>>>>>> estimation. Relax will keep on searching for
>>>>>>>>>>>>>>>>>>>>>> minimization.
>>>>>>>>>>>>>>>>>>>>>> If you are "unlucky", some of the created datasets
>>>>>>>>>>>>>>>>>>>>>> will make relax hang for a very long time.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Unfortunately, it is NOT possible to ask a processor
>>>>>>>>>>>>>>>>>>>>>> about its "current" work, when it is doing a
>>>>>>>>>>>>>>>>>>>>>> minimization for a whole
>>>>>>>>>>>>>>>>>>>>>> dataset.
>>>>>>>>>>>>>>>>>>>>>> And if it was, it would create an output of 64 spins
>>>>>>>>>>>>>>>>>>>>>> being minimized at the same time, creating a big mess,
>>>>>>>>>>>>>>>>>>>>>> since the processors
>>>>>>>>>>>>>>>>>>>>>> are working alone. When doing Monte-Carlo simulations,
>>>>>>>>>>>>>>>>>>>>>> relax are quite
>>>>>>>>>>>>>>>>>>>>>> silent. Only reporting when a whole dataset is done.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Is relax stuck in Monte-Carlo simulations?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Possible solution:
>>>>>>>>>>>>>>>>>>>>>> *) Set Monte-Carlo simulations to 3 (which is
>>>>>>>>>>>>>>>>>>>>>> minimum), and know that you have found the right
>>>>>>>>>>>>>>>>>>>>>> minimum, but the error
>>>>>>>>>>>>>>>>>>>>>> estimation of the parameters are wrong.
>>>>>>>>>>>>>>>>>>>>>> *) Carefully inspect your data, deselecting all spins
>>>>>>>>>>>>>>>>>>>>>> which have "bad data". Look at their graphs. Consider
>>>>>>>>>>>>>>>>>>>>>> working with as few
>>>>>>>>>>>>>>>>>>>>>> spins as possible, and work your way up! Working this
>>>>>>>>>>>>>>>>>>>>>> way will greatly
>>>>>>>>>>>>>>>>>>>>>> increase your productivity.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Protein 2:
>>>>>>>>>>>>>>>>>>>>>> Are you setting the bonds for the minimization
>>>>>>>>>>>>>>>>>>>>>> manually?
>>>>>>>>>>>>>>>>>>>>>> This looks like the upper/lower bonds are specified
>>>>>>>>>>>>>>>>>>>>>> wrong. This is not easy to do. How are you doing it?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> I have successfully been able to run the model-free
>>>>>>>>>>>>>>>>>>>>>>> analysis on 64 cores. The issue appears to have been I
>>>>>>>>>>>>>>>>>>>>>>> simply did not
>>>>>>>>>>>>>>>>>>>>>>> specify the spin number, so after looking at your
>>>>>>>>>>>>>>>>>>>>>>> tutorial and making the
>>>>>>>>>>>>>>>>>>>>>>> proper modifications, it ran with no complications. The
>>>>>>>>>>>>>>>>>>>>>>> results are
>>>>>>>>>>>>>>>>>>>>>>> somewhat reasonable. I decided to try to run 2 other
>>>>>>>>>>>>>>>>>>>>>>> proteins however; and
>>>>>>>>>>>>>>>>>>>>>>> I've come across problems for both again.
>>>>>>>>>>>>>>>>>>>>>>> Protein 1:
>>>>>>>>>>>>>>>>>>>>>>> I set this up just like the tutorial, and it runs
>>>>>>>>>>>>>>>>>>>>>>> with no warnings or errors; however, the run never
>>>>>>>>>>>>>>>>>>>>>>> finishes. At round_3 for
>>>>>>>>>>>>>>>>>>>>>>> the prolate model when it starts to minimize it just
>>>>>>>>>>>>>>>>>>>>>>> stops. I don't mean
>>>>>>>>>>>>>>>>>>>>>>> relax is stopped or closed, I mean it stops doing any
>>>>>>>>>>>>>>>>>>>>>>> calculations. Relax
>>>>>>>>>>>>>>>>>>>>>>> is still open, and if I run the top command, I can
>>>>>>>>>>>>>>>>>>>>>>> still see something is
>>>>>>>>>>>>>>>>>>>>>>> going on with the other cores, but nothing is being
>>>>>>>>>>>>>>>>>>>>>>> calculated. The run
>>>>>>>>>>>>>>>>>>>>>>> with 64 cores is incredibly fast (under 4 hours), so I
>>>>>>>>>>>>>>>>>>>>>>> don't think it's
>>>>>>>>>>>>>>>>>>>>>>> loading calculations or writing them, and I've left it
>>>>>>>>>>>>>>>>>>>>>>> there for over 24
>>>>>>>>>>>>>>>>>>>>>>> hours, and it's still just sorta stuck. There are no
>>>>>>>>>>>>>>>>>>>>>>> errors, no outputs, it
>>>>>>>>>>>>>>>>>>>>>>> just says its gonna start to minimize and then nothing
>>>>>>>>>>>>>>>>>>>>>>> happens after that.
>>>>>>>>>>>>>>>>>>>>>>> Protein2:
>>>>>>>>>>>>>>>>>>>>>>> This protein was a little different since the pdb
>>>>>>>>>>>>>>>>>>>>>>> structure was a crystal structure. I had to use WhatIf
>>>>>>>>>>>>>>>>>>>>>>> to add the protons
>>>>>>>>>>>>>>>>>>>>>>> onto the pdb file. The structure appears to load up
>>>>>>>>>>>>>>>>>>>>>>> fine, all the spins
>>>>>>>>>>>>>>>>>>>>>>> appear to be read, data is loaded, vectors and are
>>>>>>>>>>>>>>>>>>>>>>> calculated and define,
>>>>>>>>>>>>>>>>>>>>>>> but when I came to run the protocol this error pops up:
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/multi/processor.py",
>>>>>>>>>>>>>>>>>>>>>>> line 494, in run
>>>>>>>>>>>>>>>>>>>>>>> self.callback.init_master(self)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/multi/__init__.py",
>>>>>>>>>>>>>>>>>>>>>>> line 318, in default_init_master
>>>>>>>>>>>>>>>>>>>>>>> self.master.run()
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/relax.py", line 199,
>>>>>>>>>>>>>>>>>>>>>>> in run
>>>>>>>>>>>>>>>>>>>>>>> self.interpreter.run(self.script_file)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/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/sam2/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/sam2/relax-4.0.2/prompt/interpreter.py",
>>>>>>>>>>>>>>>>>>>>>>> line 484, in interact_script
>>>>>>>>>>>>>>>>>>>>>>> exec_script(script_file, local)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/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 192,
>>>>>>>>>>>>>>>>>>>>>>> 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/sam2/relax-4.0.2/HdeA_script.py",
>>>>>>>>>>>>>>>>>>>>>>> line 30, in <module>
>>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol(pipe_name=n
>>>>>>>>>>>>>>>>>>>>>>> ame,pipe_bundle=pipe_bundle,di
>>>>>>>>>>>>>>>>>>>>>>> ff_model=DIFF_MODEL,mf_models=
>>>>>>>>>>>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCA
>>>>>>>>>>>>>>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,
>>>>>>>>>>>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num
>>>>>>>>>>>>>>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 246, in
>>>>>>>>>>>>>>>>>>>>>>> __init__
>>>>>>>>>>>>>>>>>>>>>>> self.execute()
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 600, in execute
>>>>>>>>>>>>>>>>>>>>>>> self.multi_model(local_tm=True)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 888, in
>>>>>>>>>>>>>>>>>>>>>>> multi_model
>>>>>>>>>>>>>>>>>>>>>>> self.interpreter.minimise.grid
>>>>>>>>>>>>>>>>>>>>>>> _search(inc=self.grid_inc)
>>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/uf_objects.py",
>>>>>>>>>>>>>>>>>>>>>>> line 225, in __call__
>>>>>>>>>>>>>>>>>>>>>>> self._backend(*new_args, **uf_kargs)
>>>>>>>>>>>>>>>>>>>>>>> File
>>>>>>>>>>>>>>>>>>>>>>> "/home/sam2/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/sam2/relax-4.0.2/pipe_control/minimise.py",
>>>>>>>>>>>>>>>>>>>>>>> line 341, in grid_setup
>>>>>>>>>>>>>>>>>>>>>>> elif values[i] in [None, {}, []]:
>>>>>>>>>>>>>>>>>>>>>>> IndexError: index 0 is out of bounds for axis 0 with
>>>>>>>>>>>>>>>>>>>>>>> size 0
>>>>>>>>>>>>>>>>>>>>>>> I should mention this error pops up when it decided
>>>>>>>>>>>>>>>>>>>>>>> to calculate the first spins upper and lower bounds. So
>>>>>>>>>>>>>>>>>>>>>>> this isn't at the
>>>>>>>>>>>>>>>>>>>>>>> minimization portion of the calculation (like in the
>>>>>>>>>>>>>>>>>>>>>>> previous bug). Thanks
>>>>>>>>>>>>>>>>>>>>>>> in advance.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 14, 2016 at 6:34 AM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> To tackle this problem, I would advice to create
>>>>>>>>>>>>>>>>>>>>>>>> another bug.
>>>>>>>>>>>>>>>>>>>>>>>> Creation and closing of a bug "leaves trails",
>>>>>>>>>>>>>>>>>>>>>>>> which maybe will help another person, when googling
>>>>>>>>>>>>>>>>>>>>>>>> for the same problem.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> To help you, can you do a "relax -i" on both
>>>>>>>>>>>>>>>>>>>>>>>> computers?
>>>>>>>>>>>>>>>>>>>>>>>> That give some indication about package versions
>>>>>>>>>>>>>>>>>>>>>>>> and computer setup.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> The first thing we need to establish, is that
>>>>>>>>>>>>>>>>>>>>>>>> mpirun is working.
>>>>>>>>>>>>>>>>>>>>>>>> We have to test the installation without relax.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Can you have a look at:
>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Try the different things like:
>>>>>>>>>>>>>>>>>>>>>>>> lscpu
>>>>>>>>>>>>>>>>>>>>>>>> mpirun --report-bindings -np 11 echo "hello world"
>>>>>>>>>>>>>>>>>>>>>>>> mpirun --report-bindings -np 4 relax
>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> When we are confident about this, then we will try
>>>>>>>>>>>>>>>>>>>>>>>> make a small test script for relax.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Please try these things at both computers, and
>>>>>>>>>>>>>>>>>>>>>>>> provide 2 files with commands and output.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Then attach it to the bug report.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-14 6:40 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> So I saw the tutorial you put, and the main
>>>>>>>>>>>>>>>>>>>>>>>>> problem was I had not specified my data was only for
>>>>>>>>>>>>>>>>>>>>>>>>> the Nitrogen spins.
>>>>>>>>>>>>>>>>>>>>>>>>> After applying the spin column, my data loaded and
>>>>>>>>>>>>>>>>>>>>>>>>> relax ran model free
>>>>>>>>>>>>>>>>>>>>>>>>> with no problem. I have a script that starts and runs
>>>>>>>>>>>>>>>>>>>>>>>>> relax and model free
>>>>>>>>>>>>>>>>>>>>>>>>> all automatic, if you wish I can send it via email to
>>>>>>>>>>>>>>>>>>>>>>>>> you and you can
>>>>>>>>>>>>>>>>>>>>>>>>> upload it to the tutorial wiki page. So I can
>>>>>>>>>>>>>>>>>>>>>>>>> successfully run model-free
>>>>>>>>>>>>>>>>>>>>>>>>> in script mode for a uni-processor.
>>>>>>>>>>>>>>>>>>>>>>>>> The problem now with the multi-processor is that
>>>>>>>>>>>>>>>>>>>>>>>>> the script won't load. In the bug page I uploaded a
>>>>>>>>>>>>>>>>>>>>>>>>> screenshot where I had
>>>>>>>>>>>>>>>>>>>>>>>>> input the 'mpirun -np 4 ../relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>> command, however I had no
>>>>>>>>>>>>>>>>>>>>>>>>> output. I checked processes running in the
>>>>>>>>>>>>>>>>>>>>>>>>> background, and saw that there
>>>>>>>>>>>>>>>>>>>>>>>>> was indeed 4 processess running in the background (1
>>>>>>>>>>>>>>>>>>>>>>>>> master and 3 slaves)
>>>>>>>>>>>>>>>>>>>>>>>>> for relax; but there was no output, so I was unable
>>>>>>>>>>>>>>>>>>>>>>>>> to load any data, or
>>>>>>>>>>>>>>>>>>>>>>>>> create a pipe or anything. This was only on the
>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 24 computer, not the
>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 20. On the Fedora 20 computer, I was able to
>>>>>>>>>>>>>>>>>>>>>>>>> successfully open relax
>>>>>>>>>>>>>>>>>>>>>>>>> on a multi processor platform. I can send the
>>>>>>>>>>>>>>>>>>>>>>>>> screenshots and the relax -i
>>>>>>>>>>>>>>>>>>>>>>>>> for both computers again. I don't know why it doesn't
>>>>>>>>>>>>>>>>>>>>>>>>> work the fedora 24.
>>>>>>>>>>>>>>>>>>>>>>>>> Do you know what could be causing this?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks again in advance
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Can you send the mail again and include the
>>>>>>>>>>>>>>>>>>>>>>>>>> maillist?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Best Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Den tirsdag den 13. september 2016 skrev Mahdi,
>>>>>>>>>>>>>>>>>>>>>>>>>> Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> HI Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> So I saw the tutorial you put, and the main
>>>>>>>>>>>>>>>>>>>>>>>>>>> problem was I had not specified my data was only
>>>>>>>>>>>>>>>>>>>>>>>>>>> for the Nitrogen spins.
>>>>>>>>>>>>>>>>>>>>>>>>>>> After applying the spin column, my data loaded and
>>>>>>>>>>>>>>>>>>>>>>>>>>> relax ran model free
>>>>>>>>>>>>>>>>>>>>>>>>>>> with no problem. I have a script that starts and
>>>>>>>>>>>>>>>>>>>>>>>>>>> runs relax and model free
>>>>>>>>>>>>>>>>>>>>>>>>>>> all automatic, if you wish I can send it via email
>>>>>>>>>>>>>>>>>>>>>>>>>>> to you and you can
>>>>>>>>>>>>>>>>>>>>>>>>>>> upload it to the tutorial wiki page. So I can
>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully run model-free
>>>>>>>>>>>>>>>>>>>>>>>>>>> in script mode for a uni-processor.
>>>>>>>>>>>>>>>>>>>>>>>>>>> The problem now with the multi-processor is that
>>>>>>>>>>>>>>>>>>>>>>>>>>> the script won't load. In the bug page I uploaded a
>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot where I had
>>>>>>>>>>>>>>>>>>>>>>>>>>> input the 'mpirun -np 4 ../relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>>> command, however I had no
>>>>>>>>>>>>>>>>>>>>>>>>>>> output. I checked processes running in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> background, and saw that there
>>>>>>>>>>>>>>>>>>>>>>>>>>> was indeed 4 processess running in the background
>>>>>>>>>>>>>>>>>>>>>>>>>>> (1 master and 3 slaves)
>>>>>>>>>>>>>>>>>>>>>>>>>>> for relax; but there was no output, so I was unable
>>>>>>>>>>>>>>>>>>>>>>>>>>> to load any data, or
>>>>>>>>>>>>>>>>>>>>>>>>>>> create a pipe or anything. This was only on the
>>>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 24 computer, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 20. On the Fedora 20 computer, I was able to
>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully open relax
>>>>>>>>>>>>>>>>>>>>>>>>>>> on a multi processor platform. I can send the
>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshots and the relax -i
>>>>>>>>>>>>>>>>>>>>>>>>>>> for both computers again. I don't know why it
>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't work the fedora 24.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Do you know what could be causing this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks again in advance
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I closed the 2 bug reports as invalid.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> The data is not labelled correct.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> But this can be corrected.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see this tutorial I wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Tuto
>>>>>>>>>>>>>>>>>>>>>>>>>>>> rial_for_model-free_analysis_sam_mahdi
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this give some guidance.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> If you experience any new problems, please feel
>>>>>>>>>>>>>>>>>>>>>>>>>>>> free to ask!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> What you experience, will probably be the same
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for many.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Your feedback is valuable for the development.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please wait with using mpirun and multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>>> processors, before you are absolutely sure
>>>>>>>>>>>>>>>>>>>>>>>>>>>> that it will run on 1 processor.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Bugfixing when using multiple processors is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> nightmare....
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I just created another bug report. I simply
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> copy pasted the email, and uploaded the script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you produce another bug report.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please don't attach files to these mails as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it will strain the mailinglists.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Den lørdag den 10. september 2016 skrev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Additional question that I had, if you could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also look into this as well on Tuesday please.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have decided to try to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> write a script to automate this whole process
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (since I won't be using the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gui to do model free), and I've come across a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem. I can successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> open up relax using openmpi, and can load the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pdb file, and assign all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins and isotopes; however, it appears it will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only load one data file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (the very first one I'll have inputed in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script). I don't know if there
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is a problem with how I wrote my script. Not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only will it not load the rest
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my data sets, it won't actually run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dAuvergne's protocol either, it'll
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just load the data set and exit out of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> program. Attached is the script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I wrote for relax.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the output once relax has loaded
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script = 'model_free_sample_script.py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from time import asctime, localtime
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from auto_analyses.dauvergne_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> import dAuvergne_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DIFF_MODEL=['local_tm','sphere
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ','prolate','oblate','ellipsoid','final']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MF_MODELS=['m0','m1','m2','m3'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,'m4','m5','m6','m7','m8','m9']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOCAL_TM_MODELS=['tm0','tm1','
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tm2','tm3','tm4','tm5','tm6','
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tm7','tm7','tm8','tm9']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GRID_INC=11
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MIN_ALGOR='newton'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MC_NUM=500
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONV_LOOP=True
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe_bundle="mf(%s)"%asctime(localtime())
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name="origin-"+pipe_bundle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe.create(name,'mf',bundle=pipe_bundle)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.read_pdb('2d9j.pdb',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set_mol_name='hRGS7')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@N',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@NE1',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@H',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@HE1',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spin.isotope('15N',spin_id='@N*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spin.isotope('1H',spin_id='@H*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R2',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R2_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_A
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gnes',ri_type='NOE',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='ssNOE_Agnes',res_num_col
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> =1,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_NMRF
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R1',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_NMRFAM',res_num_col=1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_NMRF
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R2',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R2_NMRFAM',res_num_col=1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_N
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRFAM',ri_type='NOE',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='ssNOE_NMRFAM',res_num_co
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> l=1,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@N',spin_id2='@H',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> direct_bond=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@NE1',spin_id2='@HE1',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> direct_bond=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.set_dist(spin_id1='@
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N*',spin_id2='@H*',ave_dist=1.02*1e-10)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.unit_vectors()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value.set(-172*1e-6,'csa',spin_id='@N*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol(pipe_name=n
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ame,pipe_bundle=pipe_bundle,di
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ff_model=DIFF_MODEL,mf_models=
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCA
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> So it indicates that my script has loaded.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, after it loads the spins from the pdb
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, this is what happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after my first data set has been loaded:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax> relax_data.read(ri_id='R1_Agnes',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ri_type='R1', frq=599642000.0, file='R1_Agnes',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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=None)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Opening the file 'R1_Agnes' for reading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['1'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['2'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['3'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['4'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['5'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['6'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['7'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['8'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['9'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['10'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['11'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['16'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['17'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['18'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['21'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['22'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['23'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['26'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['27'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['28'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['31'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['40'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['46'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['58'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['61'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['62'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['63'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['73'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['76'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['79'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['81'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['82'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['85'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['94'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['97'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['99'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['106'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['115'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['121'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['126'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['127'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['134'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['135'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['136'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['137'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['139'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxError: The spin ID '#hRGS7:12'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponds to multiple spins, including
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '#hRGS7:12@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and '#hRGS7:12@H'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> crowlab: [~/relax-4.0.2]>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As you can see, I have all 6 data sets set
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to load, but only the very first one appears to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do so, and after it loads,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it just exits out of relax. Again, I don't know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if this is a problem with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> how I wrote the script. The Relax_script1 is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the one that I load up to run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the whole thing. The model free script.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just the script it reads once
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax has opened up. Again, I can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins are properly loaded,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the isotopes are set. It just everything
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after the first data set that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't load. Thanks again in advance.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you so much. If there is any extra
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> info you need please let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I will have some time on Tuesday, and then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I will look at it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Den onsdag den 7. september 2016 skrev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I uploaded all the files, and even added
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the entire output that i recieved using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> model free in script mode. I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> didn't know if all the files uploaded need
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to have that link, so only the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial files that were uploaded it, have it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you in advance for your help!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You should be able to upload more files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after the initial upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the comment thread, please also make
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a link to this discussion.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.gna.org/public/re
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lax-users/2016-09/threads.html#00001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for your reply. When I come
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to upload my data though, I see there are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only 4 available slots I can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload my data. I have a total of 6 data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files however, that need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploaded (3 of each frequency). I also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to upload the relax -i of 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> different computers, and the script file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I've been using for a total of 9
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that need to be uploaded. Is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> way to increase the amount I can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload, or can I upload more after the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial submission?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To solve this problem, it would be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> easier to have access to some of your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you upload to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://gna.org/bugs/?group=relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Take each of your data files, and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete all data, except 2 spins.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> description of which button you press in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the GUI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please also provide information about
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your system with:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax -i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To be added here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Cate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gory:Tutorials
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If there is a problem in relax, I will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> write a systemtest which will solve the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And the problem will never return.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If this a user error, the tutorial
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should help to prevent this, and would be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first step before
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> adding/modifying the manual.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding using mpirun.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Have a look at this page. Maybe it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello everyone,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> So I was able to set up and run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dauvergne_protocol successfully by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script in the wiki. The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem I have come across now is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> program doesn't seem to read my data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Using the gui interface I was able to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully load my data and run it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When I upload my data using the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The output file simply gives errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for amino acids I don't have data for:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the line ['1'] is invalid, the data is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is fine as relax just ignores
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> these values and continues its
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calculations. I only receive this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning for values I don't have data for.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the same thing I got when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the gui interface (the gui however
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> showed my values that I have data for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the residue it corresponds to,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script I don't receive such
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an output, I don't know whether this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is normal or not). However, since I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't get this warning for every amino
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acid, I assume this means it has read
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the values for the other amino acids.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All of my data is the same, relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings only pop up for amino acids that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't have data for. The problem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is, when I enter the dAuvergne protocol,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I get the protocol working, it starts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running local_tm however it appears
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> none of my data has been uploaded:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been deselected because of missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been deselected because of missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And I get that warning for every
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> single amino acid. From the output, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> appears to have read the file since
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it knows exactly which amino acids I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't have data for, but I don't know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why when it comes to running the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol, it tells me I havn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inputed any data. I have typed everything
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly according to the script from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the wiki. From running the protoco,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it appears everything has properly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been uploaded, structure data, magnetic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dipole interactions, csa, the data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe, the analysis variables, the python
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module imports, and setting up the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins from the pdb file. It appears the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error is from loading the actual
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On a completely unrelated side note,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have been attempting to run relax on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple processors. I have tried 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> different computers, both fedora linux.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have mpi4py and openmpi downloaded
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on both. On one, I can get relax on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple cores working (havn't been
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> able to successfully run it due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being unable to upload any data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly). On the other however, I type
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mpirun -np --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script, but I get no output. I can see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it's running in the background (top
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command), but nothing pops up, no text
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command, nothing. I typed the same
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun with the --gui, but that opened
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up nothing. On a uni-processor
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (typing in the exact same command without
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> indicating how many cores i.e. no -np
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py') it works just fine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so I don't think its my openmpi
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that's an issue. I don't know whether
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is an issue with my mpi4py or a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> personal computer issue (since on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> other
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> computer relax runs just fine on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple cores).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> P.S. when I do enter the top command
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to see what's running. My master shows
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun, and the 3 slaves display
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> python when I put -np 4, so I know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something is running in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> background. I have 8 cores.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mahdi, Sam <sam.mahdi....@my.csun.edu
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hello everyone,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am attempting to run relax on a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multi-processor mode. I have been able
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > to successfully set-up relax to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> operate in a multi-processor mode by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > the mpirun -np #ofprocessors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /location/of/relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > The problem I encounter is when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the --tee log dauvergne_protocol.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > command. I receive this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'dauvergne_protocol.py' does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I located the script file and tried
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to direct to it's path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > mpirun
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /usr/local/Relax/relax-2.2.5/relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py' --tee log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > /usr/local/Relax/relax-2.2.5/a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uto-analyses/dauvergne_protocol.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > But i received this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '/usr/local/Relax/relax-2.2.5/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > auto-analyses/dauvergne_protocol.py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Even though I have the script, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't seem to be able to locate it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > On a side note, in the manual, one
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dash doesn't actually run the command.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I.e. in the manual it displays
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -multi='mpi4py' . What it should be is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > --multi='mpi4py' . The same goes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for -tee. It should be --tee.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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
