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From: Stefano L. C. <ste...@un...> - 2025-11-07 10:34:55
|
Hello, I downloaded the Darwin dmg file, but the program does not start. I removed all restrictions for opening software, so it should open. When I click on the icon, nothing happens. Please help. Stefano Ciurli |
|
From: Stefano L. C. <ste...@un...> - 2025-11-07 08:32:35
|
Hello, I downloaded the Darwin dmg file, but the program does not start. I removed all restrictions for opening software, so it should open. When I click on the icon, nothing happens. Please help. Stefano Ciurli |
|
From: Barsukov, I. <ig...@li...> - 2025-03-02 19:53:59
|
Hello, I need to make Pymol figures that show S2 and Rex on the structure. How do I show the color-coding scale bar, similar to Fig 3 in Bieri, M., D?Auvergne, E. J., & Gooley, P. R. (2011). RelaxGUI: A new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ls motion of proteins. Journal of Biomolecular NMR, 50(2), 147-155. https://doi.org/10.1007/s10858-011-9509-1? And how do the ranges of colors correspond to S2 and Rex? I can't find any information in the manual. Thank you for your help. Best wishes Igor Dr. Igor Barsukov University of Liverpool ISMIB, BSB B138 Biosciences Building Crown Street Liverpool L69 7ZB 0151 795 4458 |
|
From: Edward d'A. <ed...@nm...> - 2025-02-20 09:08:09
|
On Sat, 8 Jun 2024 at 22:27, Kapil Modi <ka...@ny...> wrote:
>
> Hi,
>
> I'm trying to run relax on a different computer that uses windows instead of macOS and have been receiving this error when trying to run the newest version of relax (5.1,0).
>
> ImportError: ImportError('DLL load failed while importing relax_fit: The specified module could not be found.') Relaxation curve fitting is unavailable, try compiling the C modules.
>
> I looked through the mailing lists and saw that the issue was present back in 2012-2013 but I wasn't sure if it was resolved and if so, how that could be resolved.
>
> Here is the output for relax -i
>
> Name Installed Version Path
>
> minfx True 1.0.12 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\minfx-1.0.12-py3.12.egg\minfx
> bmrblib True 1.0.4 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\bmrblib-1.0.4-py3.12.egg\bmrblib
> numpy True 1.26.4 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\numpy
> scipy True 1.13.1 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\scipy
> wxPython True 4.2.1 msw (phoenix) wxWidgets 3.2.2.1 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\wx
> matplotlib True 3.9.0 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\matplotlib
> mpi4py True 3.1.6 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\mpi4py
> epydoc True 3.0.1 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\epydoc
> optparse True 1.5.3 C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\optparse.py
> readline True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\readline.py
> profile True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\profile.py
> bz2 True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\bz2.py
> gzip True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\gzip.py
> io True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\io.py
> xml True () C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\xml\__init__.py
> xml.dom.minidom True C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\xml\dom\minidom.py
>
> relax information:
> Version: 5.1.0
> Processor fabric: Uni-processor.
>
> relax C modules:
>
> Module Compiled File type Path
> target_functions.relax_fit False
>
> Any help would be greatly appreciated!
Hi Kapil,
Sorry, I missed your original message. It was automatically put into
the wrong folder. Have you managed to resolve this issue? According
to the information printout, you do not have the relaxation
curve-fitting C modules compiled (or your system architecture does not
match the binary compiled module). Which version of relax did you
install?
Regards,
Edward
|
|
From: Edward d'A. <ed...@nm...> - 2025-02-20 09:03:30
|
Hi James!
Welcome to the relax mailing lists! Please note that the Gna! mailing
lists have been shut down for almost 2 decades now. The correct
address is in the CC. The first thing you'll need is to install Python
on Windows. You'll then need to install a number of scientific Python
packages (numpy and scipy). For the graphical user interface, the
Python package wxPython is needed. If you'd like to use the
prompt-based interface, you could optionally install pyreadline. You
finally need to install the relax specific packages that I wrote -
minfx and bmrblib [1]. Python and all these packages have download
links at:
http://www.nmr-relax.com/download.html#Dependencies
Installing Python on Windows is straightforward if you have the
privileges to install software. If you need over-the-top,
ridiculously complicated instructions, here are the official ones:
https://docs.python.org/3/using/windows.html
To install packages, you can use these official instructions:
https://packaging.python.org/en/latest/tutorials/installing-packages/
Minfx and bmrblib will need to be manually downloaded and installed as
local archives (https://packaging.python.org/en/latest/tutorials/installing-packages/#installing-from-local-archives).
I hope this information helps.
Regards,
Edward
[1] Minfx: https://sourceforge.net/projects/minfx/
Bmrblib: https://sourceforge.net/projects/bmrblib/
On Wed, 5 Feb 2025 at 07:52, James Nyirenda <nyi...@un...> wrote:
>
> Dear Edward, i would like to know which package is suitable for me to install on windows. I am new and want to learn how to manipulate the nmr data for analysis of protein dynamics
>
> --
> James Nyirenda (PhD). MACS, MCSZ, MZaAS
> Fulbright 2022 Alumni
> Senior Lecturer, Department of Chemistry
> School of Natural Sciences
> University of Zambia
> P.O. Box 32379
> Lusaka
> Zambia
> Mobile: +260976834695/+260966937568
> Alternate email: jam...@gm..., jam...@fu...
> https://scholar.google.com/citations?user=kvFwMyMAAAAJ&hl=en
> https://orcid.org/0000-0001-7122-3189
> https://www.scopus.com/authid/detail.uri?authorId=36463905100
> http://catalog.lib.kyushu-u.ac.jp/en/recordID/26441
> Contact Person UNZA-AIIKS Partnership
>
>
>
> University of Zambia
>
> Great East Road Campus, Lusaka
>
> www.unza.zm
>
> CONFIDENTIAL NOTICE: This message (and its attachments) may contain confidential information. Any unauthorized use or disclosure is prohibited.
> If you have received this communication in error, please notify us immediately by responding to this email and then delete it from your system.
|
|
From: Kapil M. <ka...@ny...> - 2024-06-08 20:27:59
|
Hi,
I'm trying to run relax on a different computer that uses windows instead
of macOS and have been receiving this error when trying to run the newest
version of relax (5.1,0).
ImportError: ImportError('DLL load failed while importing relax_fit: The
specified module could not be found.') Relaxation curve fitting is
unavailable, try compiling the C modules.
I looked through the mailing lists and saw that the issue was present back
in 2012-2013 but I wasn't sure if it was resolved and if so, how that could
be resolved.
Here is the output for relax -i
Name Installed Version Path
minfx True 1.0.12
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\minfx-1.0.12-py3.12.egg\minfx
bmrblib True 1.0.4
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\bmrblib-1.0.4-py3.12.egg\bmrblib
numpy True 1.26.4
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\numpy
scipy True 1.13.1
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\scipy
wxPython True 4.2.1 msw (phoenix) wxWidgets 3.2.2.1
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\wx
matplotlib True 3.9.0
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\matplotlib
mpi4py True 3.1.6
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\mpi4py
epydoc True 3.0.1
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\epydoc
optparse True 1.5.3
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\optparse.py
readline True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\site-packages\readline.py
profile True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\profile.py
bz2 True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\bz2.py
gzip True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\gzip.py
io True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\io.py
xml True ()
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\xml\__init__.py
xml.dom.minidom True
C:\Users\kapil\AppData\Local\Programs\Python\Python312\Lib\xml\dom\minidom.py
relax information:
Version: 5.1.0
Processor fabric: Uni-processor.
relax C modules:
Module Compiled File type Path
target_functions.relax_fit False
Any help would be greatly appreciated!
Best,
Kapil
|
|
From: Kapil M. <ka...@ny...> - 2024-06-08 20:16:19
|
I see, that makes a lot of sense, thank you! On Mon, Jun 3, 2024 at 5:52 AM Edward d'Auvergne <ed...@nm...> wrote: > On Sat, 1 Jun 2024 at 17:23, Kapil Modi <ka...@ny...> wrote: > > Ah, I'm sorry for not being clear. > > > > When using the GUI and loading the example PDB file in the demo R2 > directory, the spin viewer would generate 2 molecules, both of which are > identical. It might be because I am not specifying something about the PDB > file. > > > > I redid the spin states this time specifying the name of the molecule to > be Ap4Aase and it only generated one spin state this time. So I'm guessing > I need to be specify the name of the molecule to be read from the PDB file? > > > > Cheers, > > Kapil > > > > On Fri, May 31, 2024 at 12:41 PM Kapil Modi <ka...@ny...> wrote: > >> > >> I'm unsure if screenshots work but I'll explain in case they don't. > When using the GUI and loading the example PDB file in the demo R2 > directory, the file spin viewer would generate 2 molecules, both of which > are identical. It might be because I am not specifying something about the > PDB file. I redid the spin states this time specifying the name of the > molecule to be Ap4Aase and it only generated one spin state this time. So > I'm guessing I need to be specify the name of the molecule to be read from > the PDB file? > > Hi, > > I think one of the above messages didn't make it to the mailing list. > I guess there was a problem with attaching a file. This is disabled > by default to avoid too much strain on the open source infrastructure. > > I've just tested running the analysis through the GUI and I think > there might be an issue with the way you worked through the wizard. > On the page to load the PDB file, you have both an 'Apply' and 'Next' > button. Both of these will cause the PDB file to be loaded by > executing the structure.read_pdf user function. This is deliberate, > as there are cases where you want to load models or structures > one-by-one out of a PDB file and change their numbering or for > converting between individual structures to models or reverse. So if > you accidentally load the molecule twice using the 'Apply' button, it > is safe to delete all but the first. This is also why there is a > 'Skip' button, so you can avoid loading it a second time. > > Regards, > > Edward > |
|
From: Edward d'A. <ed...@nm...> - 2024-06-03 09:51:34
|
On Sat, 1 Jun 2024 at 17:23, Kapil Modi <ka...@ny...> wrote: > Ah, I'm sorry for not being clear. > > When using the GUI and loading the example PDB file in the demo R2 directory, the spin viewer would generate 2 molecules, both of which are identical. It might be because I am not specifying something about the PDB file. > > I redid the spin states this time specifying the name of the molecule to be Ap4Aase and it only generated one spin state this time. So I'm guessing I need to be specify the name of the molecule to be read from the PDB file? > > Cheers, > Kapil > > On Fri, May 31, 2024 at 12:41 PM Kapil Modi <ka...@ny...> wrote: >> >> I'm unsure if screenshots work but I'll explain in case they don't. When using the GUI and loading the example PDB file in the demo R2 directory, the file spin viewer would generate 2 molecules, both of which are identical. It might be because I am not specifying something about the PDB file. I redid the spin states this time specifying the name of the molecule to be Ap4Aase and it only generated one spin state this time. So I'm guessing I need to be specify the name of the molecule to be read from the PDB file? Hi, I think one of the above messages didn't make it to the mailing list. I guess there was a problem with attaching a file. This is disabled by default to avoid too much strain on the open source infrastructure. I've just tested running the analysis through the GUI and I think there might be an issue with the way you worked through the wizard. On the page to load the PDB file, you have both an 'Apply' and 'Next' button. Both of these will cause the PDB file to be loaded by executing the structure.read_pdf user function. This is deliberate, as there are cases where you want to load models or structures one-by-one out of a PDB file and change their numbering or for converting between individual structures to models or reverse. So if you accidentally load the molecule twice using the 'Apply' button, it is safe to delete all but the first. This is also why there is a 'Skip' button, so you can avoid loading it a second time. Regards, Edward |
|
From: Kapil M. <ka...@ny...> - 2024-06-02 15:03:19
|
Hi again, Sorry for the double post but I resolved the issue. I realized I forgot to deselect the unresolved spins which was causing the program to attempt to optimize for them. Best, Kapil On Sat, Jun 1, 2024 at 4:02 PM Kapil Modi <ka...@ny...> wrote: > Hello, > > I'm experiencing an issue where the Line Search optimization for my set up > takes an extremely long amount of time and seems to iterate well past > 1,000,000 values for k. I set up my experiment exactly the same as in the > relax_fit script. > > Here's the exact spot where the error occurs. > > Fitting to spin '#Ap4Aase_new_3_mol1:3@N' > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > Newton minimisation > > ~~~~~~~~~~~~~~~~~~~ > > Line search: Backtracking line search. > > Hessian modification: The Gill, Murray, and Wright modified Cholesky > algorithm. > > > k: 0 xk: [ 20, 2000] fk: 10.5392026372 > > > k: 100 xk: [ 494.4015814, 20474015.74] fk: 6.96842623012 > > > k: 200 xk: [ 517.0492257, 30502358.26] fk: 6.9683206805 > > > k: 300 xk: [ 527.0537514, 36375387.07] fk: 6.96828589187 > > > k: 400 xk: [ 533.5623637, 40790463.33] fk: 6.96826633601 > > > k: 500 xk: [ 538.3959132, 44412527.99] fk: 6.96825319617 > > > k: 600 xk: [ 542.2426565, 47523593.85] fk: 6.96824350921 > > > k: 700 xk: [ 545.4380817, 50272959.33] fk: 6.96823594648 > > > k: 800 xk: [ 548.1711776, 52750386.01] fk: 6.96822980706 > > > k: 900 xk: [ 550.5589954, 55014551.85] fk: 6.96822467975 > > > k: 1000 xk: [ 552.6790841, 57106170.59] fk: 6.96822030448 > > > I've also noticed that my run will optimize at an extra spin at residue 3 > whereas the demo run does not load that spin during execution. > > > Is this a setup issue on my part? I'm also running relax on macOS. > > > Best, > Kapil > |
|
From: Kapil M. <ka...@ny...> - 2024-06-01 20:03:40
|
Hello, I'm experiencing an issue where the Line Search optimization for my set up takes an extremely long amount of time and seems to iterate well past 1,000,000 values for k. I set up my experiment exactly the same as in the relax_fit script. Here's the exact spot where the error occurs. Fitting to spin '#Ap4Aase_new_3_mol1:3@N' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: [ 20, 2000] fk: 10.5392026372 k: 100 xk: [ 494.4015814, 20474015.74] fk: 6.96842623012 k: 200 xk: [ 517.0492257, 30502358.26] fk: 6.9683206805 k: 300 xk: [ 527.0537514, 36375387.07] fk: 6.96828589187 k: 400 xk: [ 533.5623637, 40790463.33] fk: 6.96826633601 k: 500 xk: [ 538.3959132, 44412527.99] fk: 6.96825319617 k: 600 xk: [ 542.2426565, 47523593.85] fk: 6.96824350921 k: 700 xk: [ 545.4380817, 50272959.33] fk: 6.96823594648 k: 800 xk: [ 548.1711776, 52750386.01] fk: 6.96822980706 k: 900 xk: [ 550.5589954, 55014551.85] fk: 6.96822467975 k: 1000 xk: [ 552.6790841, 57106170.59] fk: 6.96822030448 I've also noticed that my run will optimize at an extra spin at residue 3 whereas the demo run does not load that spin during execution. Is this a setup issue on my part? I'm also running relax on macOS. Best, Kapil |
|
From: Kapil M. <ka...@ny...> - 2024-06-01 15:23:59
|
Ah, I'm sorry for not being clear. When using the GUI and loading the example PDB file in the demo R2 directory, the spin viewer would generate 2 molecules, both of which are identical. It might be because I am not specifying something about the PDB file. I redid the spin states this time specifying the name of the molecule to be Ap4Aase and it only generated one spin state this time. So I'm guessing I need to be specify the name of the molecule to be read from the PDB file? Cheers, Kapil On Fri, May 31, 2024 at 12:41 PM Kapil Modi <ka...@ny...> wrote: > I'm unsure if screenshots work but I'll explain in case they don't. When > using the GUI and loading the example PDB file in the demo R2 directory, > the file spin viewer would generate 2 molecules, both of which are > identical. It might be because I am not specifying something about the PDB > file. I redid the spin states this time specifying the name of the molecule > to be Ap4Aase and it only generated one spin state this time. So I'm > guessing I need to be specify the name of the molecule to be read from the > PDB file? > > Cheers, > Kapil > > On Fri, May 31, 2024 at 11:25 AM Edward d'Auvergne <ed...@nm...> > wrote: > >> On Fri, 31 May 2024 at 16:54, Kapil Modi <ka...@ny...> wrote: >> > Thank you for the response and the guidance! Also, I apologize if I am >> once again sending this message incorrectly because I am also new to >> SourceForge. >> >> Not a problem. The messages are working correctly now. >> >> > While running test data using the Ap4Ase for the R2 demo, I noticed >> that there would be two molecules loaded in the spin states that had the >> exact same residues and spins. >> >> In the demo repository, there is a single NMR model with a single >> polypeptide in the PDB file: >> >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_nmr-2Drelax_relax-2Ddemo_ci_master_tree_R2_Ap4Aase_Ap4Aase-5Fnew-5F3.pdb&d=DwIBaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=7ULZ3RgKGAAE_RtB3PHsQg&m=tedO9SRMV_M2Nu5ehUoXH03y6XSd0AHM-55ZJXjvM9SCOuO4raUoUlgEyaprD0GA&s=iLWSBQTb1V5kVWW7BmnsXsl1HrpCi8H8fxUUnzvNf7I&e= >> >> In which file within the demo do you see two molecules? You should >> use this PDB file with the R2 demo data. As a hint, in the analysis/ >> directory, you can find the relax_fit.py script which shows you >> exactly how to perform the analysis. >> >> >> > I deleted one of the molecules for the execution of my data because I >> assumed that the PDB file only contains one molecule. Is there an error I'm >> making in my setup that causes this to occur? >> >> Are you talking about your measured data and a real PDB structure? If >> so, is the PDB a set of NMR models or an X-ray PDB with multiple >> structures? I'm a little confused as to what is going on. >> >> Regards, >> >> Edward >> > |
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From: Edward d'A. <ed...@nm...> - 2024-05-31 15:25:35
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On Fri, 31 May 2024 at 16:54, Kapil Modi <ka...@ny...> wrote:
> Thank you for the response and the guidance! Also, I apologize if I am once again sending this message incorrectly because I am also new to SourceForge.
Not a problem. The messages are working correctly now.
> While running test data using the Ap4Ase for the R2 demo, I noticed that there would be two molecules loaded in the spin states that had the exact same residues and spins.
In the demo repository, there is a single NMR model with a single
polypeptide in the PDB file:
https://sourceforge.net/p/nmr-relax/relax-demo/ci/master/tree/R2/Ap4Aase/Ap4Aase_new_3.pdb
In which file within the demo do you see two molecules? You should
use this PDB file with the R2 demo data. As a hint, in the analysis/
directory, you can find the relax_fit.py script which shows you
exactly how to perform the analysis.
> I deleted one of the molecules for the execution of my data because I assumed that the PDB file only contains one molecule. Is there an error I'm making in my setup that causes this to occur?
Are you talking about your measured data and a real PDB structure? If
so, is the PDB a set of NMR models or an X-ray PDB with multiple
structures? I'm a little confused as to what is going on.
Regards,
Edward
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From: Kapil M. <ka...@ny...> - 2024-05-31 14:54:48
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Hi Edward, Thank you for the response and the guidance! Also, I apologize if I am once again sending this message incorrectly because I am also new to SourceForge. While running test data using the Ap4Ase for the R2 demo, I noticed that there would be two molecules loaded in the spin states that had the exact same residues and spins. I deleted one of the molecules for the execution of my data because I assumed that the PDB file only contains one molecule. Is there an error I'm making in my setup that causes this to occur? Cheers, Kapil On Fri, May 24, 2024 at 5:57 AM Edward d'Auvergne <ed...@nm...> wrote: > Hi Kapil, > > Welcome to the relax mailing lists! This is the correct place to ask > questions about using relax. To learn how to use relax, the test > suite data is not the best way to start. This consists of highly > truncated minimal data sets that are specifically modified to run > tests quickly. It can be quite confusing at times. The best way to > start would be to use the relax demo repository: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_nmr-2Drelax_relax-2Ddemo_ci_master_tree_&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=7ULZ3RgKGAAE_RtB3PHsQg&m=SqDLzYqs3MLxB30JgIFjfEF_GJlgNc7whENDgkPm9CEh0f5D4GMieZUGRfQ0bVh8&s=wGhaP3u4Qu0VtpIWlsqq_pXbGjTEAU6FdXxBrDK42J0&e= > > You can either checkout the repository (if you know how to do that), > or simply click on 'download a snapshot' in the web interface. Within > the subdirectories of this demo repository, I have written README > files that contain all the information you need to perform a > steady-state NOE analysis, Rx relaxation rate curve-fitting analysis, > a full relaxation dispersion analysis, or a full model-free analysis. > This repository can be used in combination with the corresponding > analysis type chapters of the relax manual to see how to use the > scripting/prompt interface, or the graphical user interface. I hope > this helps. > > Regards, > > Edward > > > > > On Thu, 23 May 2024 at 22:18, Kapil Modi <ka...@ny...> wrote: > > > > Hello there! > > > > I hope this is the right way to send this email. > > > > I am new to relax-NMR and am trying to understand the general experiment > set up when running analyses. I have been trying to use some of the data in > the test-suite under the peak list tab. (xeasy_r1_20ms.text this > specifically). I am able to load the spins from the list, but when trying > to load spectral data, I go through the wizard but am met with a "spectral > data not loaded" error when trying to execute the program. Has anyone else > encountered this issue when starting, and would you be able to guide me in > what I am doing wrong? > > > > Best, > > Kapil > > _______________________________________________ > > nmr-relax-users mailing list > > nmr...@li... > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_nmr-2Drelax-2Dusers&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=7ULZ3RgKGAAE_RtB3PHsQg&m=SqDLzYqs3MLxB30JgIFjfEF_GJlgNc7whENDgkPm9CEh0f5D4GMieZUGRfQ0bVh8&s=bdlo0ZMFB0zjFHZRddJHuyGNza0wtu1UgEPHrjSl45A&e= > |
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From: Kapil M. <ka...@ny...> - 2024-05-23 20:18:36
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Hello there! I hope this is the right way to send this email. I am new to relax-NMR and am trying to understand the general experiment set up when running analyses. I have been trying to use some of the data in the test-suite under the peak list tab. (xeasy_r1_20ms.text this specifically). I am able to load the spins from the list, but when trying to load spectral data, I go through the wizard but am met with a "spectral data not loaded" error when trying to execute the program. Has anyone else encountered this issue when starting, and would you be able to guide me in what I am doing wrong? Best, Kapil |
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From: Mark B. <mar...@tu...> - 2023-12-16 16:58:05
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Dear Edward,
I'm trying to run a global fit on some 15N CPMG relaxation dispersion
data. I have already run the residues with individual fits and am using
a script (copied below), based on one in the relax example scripts
folder. At the moment the script fails due to the size of the grid
search. I thought that by loading existing single-residue fits and using
the relax_disp.parameter_copy function, this should reduce the size of
the grid search. Could you provide any suggestions?
Many thanks,
Mark
---------------------------------------------------------------------------
# Python module imports.
from os import getcwd, sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.dispersion.variables import MODEL_R2EFF, MODEL_CR72,
MODEL_CR72_FULL, MODEL_TSMFK01, MODEL_IT99, MODEL_B14_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR_FULL
from pipe_control.mol_res_spin import spin_loop
#########################################
#### Setup
# The pipe names.
if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle') and
hasattr(ds, 'pipe_type') and hasattr(ds, 'pipe_bundle_cluster')):
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
ds.pipe_type = 'relax_disp'
ds.pipe_bundle_cluster = 'cluster'
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
# The models to analyse.
print(hasattr(ds,'models'))
if not hasattr(ds, 'models'):
if 0:
ds.models = [MODEL_R2EFF, MODEL_CR72, MODEL_CR72_FULL]
else:
ds.models = [MODEL_CR72]
print(ds.models)
# The number of increments per parameter, to split up the search
interval in grid search.
# This is not used, when pointing to a previous result directory.
# Then an average of the previous values will be used.
if not hasattr(ds, 'grid_inc'):
ds.grid_inc = 11
# The number of Monte-Carlo simulations for estimating the error of the
parameters of the fitted models.
if not hasattr(ds, 'mc_sim_num'):
ds.mc_sim_num = 10
# The model selection technique. Either: 'AIC', 'AICc', 'BIC'
if not hasattr(ds, 'modsel'):
ds.modsel = 'AIC'
# The previous result directory with R2eff values.
if not hasattr(ds, 'pre_run_dir'):
ds.pre_run_dir = './fit_CR72_final/' + sep + 'R2eff'
print(ds.pre_run_dir)
# The result directory.
if not hasattr(ds, 'results_dir'):
ds.results_dir = './fit_clustered_CR72/'
## The optimisation function tolerance.
## This is set to the standard value, and should not be changed.
#if not hasattr(ds, 'opt_func_tol'):
# ds.opt_func_tol = 1e-25
#Relax_disp.opt_func_tol = ds.opt_func_tol
#if not hasattr(ds, 'opt_max_iterations'):
# ds.opt_max_iterations = int(1e7)
#Relax_disp.opt_max_iterations = ds.opt_max_iteration
#########################################
# Create the data pipe.
ini_pipe_name = '%s - %s' % (ds.models[0], ds.pipe_bundle)
pipe.create(pipe_name=ini_pipe_name, bundle=ds.pipe_bundle,
pipe_type=ds.pipe_type)
# Load the previous results into the base pipe.
results.read(file='results', dir=ds.pre_run_dir)
# Create a new pipe, where the clustering analysis will happen.
# We will copy the pipe to get all information.
pipe.copy(pipe_from=ini_pipe_name, pipe_to=ds.pipe_name,
bundle_to=ds.pipe_bundle_cluster)
pipe.switch(ds.pipe_name)
#pipe.display()
#Spin clusters
N15_cluster_remove = [":2@N",":3@N",":4@N"]
for spin_id in N15_cluster_remove:
relax_disp.cluster('N15_cluster', spin_id)
# See the clustering in the current data pipe "cdp".
for key in cdp.clustering:
print(key, cdp.clustering[key])
# Print parameter kex before copying.
#for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
# print(cur_spin.kex)
## Make advanced parameter copy.
# It is more advanced than the value.copy user function, in that
clustering is taken into account.
# When the destination data pipe has spin clusters defined, then the new
parameter values, when required, will be taken as the median value.
relax_disp.parameter_copy(pipe_from=ini_pipe_name, pipe_to=ds.pipe_name)
pipe.display()
# Run the analysis.
Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle_cluster,
results_dir=ds.results_dir, models=ds.models, grid_inc=ds.grid_inc,
mc_sim_num=ds.mc_sim_num, modsel=ds.modsel)
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From: Edward d'A. <ed...@nm...> - 2022-11-30 09:32:18
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Hi Paul,
Great to hear from you again! I hope all is well over there in
Vienna. Sorry for the super late reply - I've been flat out lately.
As for your questions:
On Wed, 26 Oct 2022 at 17:44, Paul SCHANDA <pau...@is...> wrote:
> Hi,
>
> I am running into troubles with R1rho dispersion fits. In brief, we get totally unrealistic values for phi_ex (>10000) and k_ex (<1 s-1).
> It seems that the default parameter limits for phi_ex are such that there is only a lower bound (0) but no upper bound. This can result in physically totally meaningless situations, like a strong R1rho dispersion profile, with a fitted exchange rate constants of 0.2 s-1….
> I would like to have some control over the grid search and the analysis.
>
> My questions:
> * does anyone know how to set/change the grid parameter range? Has anyone run into similar issues?
For the initial grid search, in a custom script you can simply pass in
a list of numbers for the lower bounds and or upper bounds. This
issue is quite common and most people end up reporting that this
happens for peaks that are very weak at the very start, so that the
fit simply fails no matter what you do. This may not be the case for
your data. What would be best is to actually map out the parameter
optimisation space and visualise it in 3D. If you install the
ancient, yet still very powerful, OpenDX software (the code is still
on SourceForge and a number of Linux distributions package it). You
can then use the relax dx.map user function to visualise the
optimisation space:
https://www.nmr-relax.com/manual/dx_map.html
We do need to implement other ways of visualising this in relax, for
example with mathplotlib which is currently an optional dependency,
but that has not materialised. For anyone interested, it should be a
pretty easy task to duplicate dx.map to a new mathplotlib.map.
> * does anyone have a script to do the analysis without going through the auto-analysis? The manual is (for me) not useful to design the analysis.
The best way is to copy the auto-analysis file itself
(auto_analyses/relax_disp.py) and modify that as you see fit. You can
have this sitting next to your analysis script (or even copied and
pasted inside it) and, instead of importing the auto-analysis with:
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
you can import your modified auto-analysis with:
# My module imports.
from my_relax_disp_auto_analysis import Relax_disp
That way you can go in and add upper (and maybe lower) bounds where
the grid search user function is called
(self.interpreter.minimise.grid_search()).
However I'd first recommend mapping out the optimisation space to see
if you have a minimum anywhere in there first. This will save a lot of
time. In relaxation dispersion, as far as anyone has seen that I am
aware of, the minimisation space is very simple. You have a single
very broad quadratic minimum. There are no multi-minima spaces, long
twisting tunnels, or banana problems (that's a real thing) in the
optimization space. So directly visualising the space is incredibly
powerful and will shape your strategy for dealing with the data point.
Regards,
Edward
P. S. If you need upper bounds on optimisation, for now you'll need
to modify the relax source code itself. We had plans many years ago
to open up this interface via new user functions, however that work
never materialised. See the function linear_constraints() in the file
specific_analyses/relax_disp/parameters.py for the hard-coded values.
|
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From: Paul S. <pau...@is...> - 2022-10-26 15:44:12
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Hi, I am running into troubles with R1rho dispersion fits. In brief, we get totally unrealistic values for phi_ex (>10000) and k_ex (<1 s-1). It seems that the default parameter limits for phi_ex are such that there is only a lower bound (0) but no upper bound. This can result in physically totally meaningless situations, like a strong R1rho dispersion profile, with a fitted exchange rate constants of 0.2 s-1…. I would like to have some control over the grid search and the analysis. My questions: * does anyone know how to set/change the grid parameter range? Has anyone run into similar issues? * does anyone have a script to do the analysis without going through the auto-analysis? The manual is (for me) not useful to design the analysis. Thanks Paul 1. |
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From: Edward d'A. <ed...@nm...> - 2022-07-28 19:46:13
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On Thu, 28 Jul 2022 at 16:52, Johan Wallerstein <joh...@gu...> wrote: > > I appreciate these comments and thoughts on the subject, I’m soon back to working mode and will then go more into the topic. If I find something of interest I'll post it. No problems! Note that I'll soon be on summer holiday for the most of August on a beach in France, so don't be surprised if you don't find me very responsive ;) Regards, Edward |
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From: Johan W. <joh...@gu...> - 2022-07-28 14:52:16
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Hi, Thank you very much. I apologise for very late reply, the main reason for my delayed reply is that my summer holiday with kids/family started in beginning of July. For some reason I believe it is good for me to decouple from the job once in a while. See comments further down: On 2 Jul 2022, at 10:06, Edward d'Auvergne <ed...@nm...<mailto:ed...@nm...>> wrote: On Thu, 30 Jun 2022 at 08:19, Johan Wallerstein <joh...@gu...<mailto:joh...@gu...>> wrote: Hi, I perform CPMG-RD cluster fitting using relax, cluster refer to grouping several residues (between 3 to 14 residues) for data from a 45 kDa protein. The software is a good tool for doing this analysis. I marginally adjust the core protocol with the header """Script for performing a full relaxation dispersion analysis using CPMG-type data.""" I use only the CR72-model and I have a PRE_RUN_DIR from a run with individual residues. I use duplicates for error estimation, on both the 800 MHz and 900 MHz data set, and AIC for model selection. When I analyse the clustered data I’m curious to get R2eff_(back_calc) for each data point. I clarify my main question by attaching some of my data. ########### For residue 530, when I do individual fit I get this output. From the log-file: ——— The spin cluster [':530@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 2 25 21.11216 25.11216 CR72 - relax_disp 5 25 13.93686 23.93686 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— The file ‘disp_530_N.out’ in /final gives the following data table: # Experiment_name Field_strength_(MHz) Disp_point_(Hz) R2eff_(measured) R2eff_(back_calc) R2eff_errors 'SQ CPMG' 799.870000000 25.000000 17.523783179912268 16.953711340740483 0.831932502443187 'SQ CPMG' 799.870000000 50.000000 16.513029763549930 16.914478241596726 0.805586049587058 'SQ CPMG' 799.870000000 75.000000 16.920353186819355 16.875245142453196 0.816049323427317 'SQ CPMG' 799.870000000 100.000000 16.667402888129434 16.836012043882192 0.809527349094067 'SQ CPMG' 799.870000000 150.000000 16.454146002323920 16.757546676539960 0.804090431533660 'SQ CPMG' 799.870000000 200.000000 16.359623786385509 16.679111600438773 0.801698521274394 'SQ CPMG' 799.870000000 300.000000 15.525257427659495 16.523477804972345 0.781054888748662 'SQ CPMG' 799.870000000 350.000000 16.609858567997016 16.447662190184474 0.808054742944598 'SQ CPMG' 799.870000000 400.000000 16.844330710216166 16.374401478154368 0.814080812205130 'SQ CPMG' 799.870000000 500.000000 17.414128601521103 16.238705811895670 0.829011905615397 'SQ CPMG' 799.870000000 600.000000 16.093980388806685 16.120475644003818 0.795034804815920 'SQ CPMG' 799.870000000 800.000000 15.988036247232372 15.937187687218284 0.792401090807446 'SQ CPMG' 799.870000000 1000.000000 15.732649459437805 15.811741022120714 0.786107934589661 'SQ CPMG' 900.130000000 57.000000 19.386713898811351 20.163621643615215 0.801212497068354 'SQ CPMG' 900.130000000 114.000000 21.873502893081564 20.050473540803750 0.859660006101508 'SQ CPMG' 900.130000000 171.000000 19.133628964210569 19.937331394199191 0.795598311646227 'SQ CPMG' 900.130000000 228.000000 20.497316023709256 19.824330722189416 0.826567798566107 'SQ CPMG' 900.130000000 285.000000 20.091262254550443 19.712140304427066 0.817160298225920 'SQ CPMG' 900.130000000 400.000000 19.177817248045365 19.494278567900892 0.796574222459005 'SQ CPMG' 900.130000000 514.000000 19.111643299707755 19.300194513689348 0.795113430566997 'SQ CPMG' 900.130000000 628.000000 18.432363807026835 19.135138271300775 0.780352695478047 'SQ CPMG' 900.130000000 742.000000 19.383070346051138 18.999531230125285 0.801131245976946 'SQ CPMG' 900.130000000 857.000000 18.560791856291317 18.889165645990943 0.783110910382522 'SQ CPMG' 900.130000000 971.000000 18.810639108776328 18.801416118812085 0.788520121686263 'SQ CPMG' 900.130000000 1085.000000 18.943973311789268 18.730884832131551 0.791430360141496 ########### For a cluster fit (including residue 530) I get this output from the log-file: ——— The spin cluster [':530@N', ':536@N', ':537@N', ':538@N', ':550@N', ':551@N', ':552@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 14 175 458.66116 486.66116 CR72 - relax_disp 23 175 117.29418 163.29418 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— This looks reasonable. This is 7 spins, so on average, 117.29/7 = 16.76, which is a little more than the single spin value of 13.94. But there is no corresponding data table. Do you mean that there is no ‘disp_530_N.out’ file for the clustered analysis? The file is there, I did not realise that the file disp_???.out in a clustered analysis contains the new data. I think I should have understood this… ########### QUESTION 1: Is it possible to get, or easily create a table with, in my case, 175 R2eff_(back_calc) for the cluster, so that I can get better resolution on the Chi2 = 117.29418 above ? And possibly study how a single residue affect the cluster fitting. Try the value.write() user function: https://www.nmr-relax.com/manual/value_write.html Make sure to set the 'bc' flag to True. Thanks! QUESTION 2: Are there any reference to methods used for doing efficient selection of residues included in the cluster? There is obviously an immense number of combinations of residues to make clusters in a normal size protein. I consider making a program/script for this process and would be curious to get some inspiration. As far as I am aware, human logic is used for this process. You identify a rigid moving unit in your system yourself with similar dispersion results and then use clustering on that. I would assume that an automated system to find clusters would be computationally very expensive, despite being able to run on a computer cluster via MPI. And that such a project would take up half or more of a PhD student's time. Then again, I wouldn't be surprised if there is now a publication exploring this concept. If you do find one, I'd be interested in hearing about it. I appreciate these comments and thoughts on the subject, I’m soon back to working mode and will then go more into the topic. If I find something of interest I'll post it. Before holiday I “somehow" managed to create a semi-automatic approach to run all possible combinations of a set of residues in relax, ie the number of combinations of N things taken K at a time. Lets say the cluster I want to investigate consists of 8 residues (N) but I’m not confident in that selection. The 8 residues is the core cluster and I let relax run the combinations of 6 (K) of these 8 core residues, it turns out to be 28 relax runs. I’m not sure this is a good approach, I need to evaluate it. A problem with the data is the low signal / noise ratio. It is a large protein. This has of course many consequences for my CPMG-RD analysis with relax. (28 comes from N!/K!(N-K)! ) Best regards Johan On 2 Jul 2022, at 10:06, Edward d'Auvergne <ed...@nm...<mailto:ed...@nm...>> wrote: On Thu, 30 Jun 2022 at 08:19, Johan Wallerstein <joh...@gu...<mailto:joh...@gu...>> wrote: Hi, I perform CPMG-RD cluster fitting using relax, cluster refer to grouping several residues (between 3 to 14 residues) for data from a 45 kDa protein. The software is a good tool for doing this analysis. I marginally adjust the core protocol with the header """Script for performing a full relaxation dispersion analysis using CPMG-type data.""" I use only the CR72-model and I have a PRE_RUN_DIR from a run with individual residues. I use duplicates for error estimation, on both the 800 MHz and 900 MHz data set, and AIC for model selection. When I analyse the clustered data I’m curious to get R2eff_(back_calc) for each data point. I clarify my main question by attaching some of my data. ########### For residue 530, when I do individual fit I get this output. From the log-file: ——— The spin cluster [':530@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 2 25 21.11216 25.11216 CR72 - relax_disp 5 25 13.93686 23.93686 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— The file ‘disp_530_N.out’ in /final gives the following data table: # Experiment_name Field_strength_(MHz) Disp_point_(Hz) R2eff_(measured) R2eff_(back_calc) R2eff_errors 'SQ CPMG' 799.870000000 25.000000 17.523783179912268 16.953711340740483 0.831932502443187 'SQ CPMG' 799.870000000 50.000000 16.513029763549930 16.914478241596726 0.805586049587058 'SQ CPMG' 799.870000000 75.000000 16.920353186819355 16.875245142453196 0.816049323427317 'SQ CPMG' 799.870000000 100.000000 16.667402888129434 16.836012043882192 0.809527349094067 'SQ CPMG' 799.870000000 150.000000 16.454146002323920 16.757546676539960 0.804090431533660 'SQ CPMG' 799.870000000 200.000000 16.359623786385509 16.679111600438773 0.801698521274394 'SQ CPMG' 799.870000000 300.000000 15.525257427659495 16.523477804972345 0.781054888748662 'SQ CPMG' 799.870000000 350.000000 16.609858567997016 16.447662190184474 0.808054742944598 'SQ CPMG' 799.870000000 400.000000 16.844330710216166 16.374401478154368 0.814080812205130 'SQ CPMG' 799.870000000 500.000000 17.414128601521103 16.238705811895670 0.829011905615397 'SQ CPMG' 799.870000000 600.000000 16.093980388806685 16.120475644003818 0.795034804815920 'SQ CPMG' 799.870000000 800.000000 15.988036247232372 15.937187687218284 0.792401090807446 'SQ CPMG' 799.870000000 1000.000000 15.732649459437805 15.811741022120714 0.786107934589661 'SQ CPMG' 900.130000000 57.000000 19.386713898811351 20.163621643615215 0.801212497068354 'SQ CPMG' 900.130000000 114.000000 21.873502893081564 20.050473540803750 0.859660006101508 'SQ CPMG' 900.130000000 171.000000 19.133628964210569 19.937331394199191 0.795598311646227 'SQ CPMG' 900.130000000 228.000000 20.497316023709256 19.824330722189416 0.826567798566107 'SQ CPMG' 900.130000000 285.000000 20.091262254550443 19.712140304427066 0.817160298225920 'SQ CPMG' 900.130000000 400.000000 19.177817248045365 19.494278567900892 0.796574222459005 'SQ CPMG' 900.130000000 514.000000 19.111643299707755 19.300194513689348 0.795113430566997 'SQ CPMG' 900.130000000 628.000000 18.432363807026835 19.135138271300775 0.780352695478047 'SQ CPMG' 900.130000000 742.000000 19.383070346051138 18.999531230125285 0.801131245976946 'SQ CPMG' 900.130000000 857.000000 18.560791856291317 18.889165645990943 0.783110910382522 'SQ CPMG' 900.130000000 971.000000 18.810639108776328 18.801416118812085 0.788520121686263 'SQ CPMG' 900.130000000 1085.000000 18.943973311789268 18.730884832131551 0.791430360141496 ########### For a cluster fit (including residue 530) I get this output from the log-file: ——— The spin cluster [':530@N', ':536@N', ':537@N', ':538@N', ':550@N', ':551@N', ':552@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 14 175 458.66116 486.66116 CR72 - relax_disp 23 175 117.29418 163.29418 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— This looks reasonable. This is 7 spins, so on average, 117.29/7 = 16.76, which is a little more than the single spin value of 13.94. But there is no corresponding data table. Do you mean that there is no ‘disp_530_N.out’ file for the clustered analysis? ########### QUESTION 1: Is it possible to get, or easily create a table with, in my case, 175 R2eff_(back_calc) for the cluster, so that I can get better resolution on the Chi2 = 117.29418 above ? And possibly study how a single residue affect the cluster fitting. Try the value.write() user function: https://www.nmr-relax.com/manual/value_write.html Make sure to set the 'bc' flag to True. QUESTION 2: Are there any reference to methods used for doing efficient selection of residues included in the cluster? There is obviously an immense number of combinations of residues to make clusters in a normal size protein. I consider making a program/script for this process and would be curious to get some inspiration. As far as I am aware, human logic is used for this process. You identify a rigid moving unit in your system yourself with similar dispersion results and then use clustering on that. I would assume that an automated system to find clusters would be computationally very expensive, despite being able to run on a computer cluster via MPI. And that such a project would take up half or more of a PhD student's time. Then again, I wouldn't be surprised if there is now a publication exploring this concept. If you do find one, I'd be interested in hearing about it. Regards, Edward |
|
From: Edward d'A. <ed...@nm...> - 2022-07-02 11:10:08
|
On Thu, 30 Jun 2022 at 08:19, Johan Wallerstein <joh...@gu...> wrote:
>
> Hi,
>
> I perform CPMG-RD cluster fitting using relax, cluster refer to grouping several residues (between 3 to 14 residues) for data from a 45 kDa protein. The software is a good tool for doing this analysis. I marginally adjust the core protocol with the header
>
>
>
> """Script for performing a full relaxation dispersion analysis using CPMG-type data."""
>
> I use only the CR72-model and I have a PRE_RUN_DIR from a run with individual residues. I use duplicates for error estimation, on both the 800 MHz and 900 MHz data set, and AIC for model selection.
> When I analyse the clustered data I’m curious to get R2eff_(back_calc) for each data point. I clarify my main question by attaching some of my data.
>
> ###########
>
> For residue 530, when I do individual fit I get this output.
>
> From the log-file:
>
> ———
>
> The spin cluster [':530@N'].
> # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion
> No Rex - relax_disp 2 25 21.11216 25.11216
> CR72 - relax_disp 5 25 13.93686 23.93686
> The model from the data pipe 'CR72 - relax_disp' has been selected.
>
> ———
>
> The file ‘disp_530_N.out’ in /final gives the following data table:
>
> # Experiment_name Field_strength_(MHz) Disp_point_(Hz) R2eff_(measured) R2eff_(back_calc) R2eff_errors
> 'SQ CPMG' 799.870000000 25.000000 17.523783179912268 16.953711340740483 0.831932502443187
> 'SQ CPMG' 799.870000000 50.000000 16.513029763549930 16.914478241596726 0.805586049587058
> 'SQ CPMG' 799.870000000 75.000000 16.920353186819355 16.875245142453196 0.816049323427317
> 'SQ CPMG' 799.870000000 100.000000 16.667402888129434 16.836012043882192 0.809527349094067
> 'SQ CPMG' 799.870000000 150.000000 16.454146002323920 16.757546676539960 0.804090431533660
> 'SQ CPMG' 799.870000000 200.000000 16.359623786385509 16.679111600438773 0.801698521274394
> 'SQ CPMG' 799.870000000 300.000000 15.525257427659495 16.523477804972345 0.781054888748662
> 'SQ CPMG' 799.870000000 350.000000 16.609858567997016 16.447662190184474 0.808054742944598
> 'SQ CPMG' 799.870000000 400.000000 16.844330710216166 16.374401478154368 0.814080812205130
> 'SQ CPMG' 799.870000000 500.000000 17.414128601521103 16.238705811895670 0.829011905615397
> 'SQ CPMG' 799.870000000 600.000000 16.093980388806685 16.120475644003818 0.795034804815920
> 'SQ CPMG' 799.870000000 800.000000 15.988036247232372 15.937187687218284 0.792401090807446
> 'SQ CPMG' 799.870000000 1000.000000 15.732649459437805 15.811741022120714 0.786107934589661
> 'SQ CPMG' 900.130000000 57.000000 19.386713898811351 20.163621643615215 0.801212497068354
> 'SQ CPMG' 900.130000000 114.000000 21.873502893081564 20.050473540803750 0.859660006101508
> 'SQ CPMG' 900.130000000 171.000000 19.133628964210569 19.937331394199191 0.795598311646227
> 'SQ CPMG' 900.130000000 228.000000 20.497316023709256 19.824330722189416 0.826567798566107
> 'SQ CPMG' 900.130000000 285.000000 20.091262254550443 19.712140304427066 0.817160298225920
> 'SQ CPMG' 900.130000000 400.000000 19.177817248045365 19.494278567900892 0.796574222459005
> 'SQ CPMG' 900.130000000 514.000000 19.111643299707755 19.300194513689348 0.795113430566997
> 'SQ CPMG' 900.130000000 628.000000 18.432363807026835 19.135138271300775 0.780352695478047
> 'SQ CPMG' 900.130000000 742.000000 19.383070346051138 18.999531230125285 0.801131245976946
> 'SQ CPMG' 900.130000000 857.000000 18.560791856291317 18.889165645990943 0.783110910382522
> 'SQ CPMG' 900.130000000 971.000000 18.810639108776328 18.801416118812085 0.788520121686263
> 'SQ CPMG' 900.130000000 1085.000000 18.943973311789268 18.730884832131551 0.791430360141496
>
> ###########
>
> For a cluster fit (including residue 530) I get this output from the log-file:
>
> ———
>
> The spin cluster [':530@N', ':536@N', ':537@N', ':538@N', ':550@N', ':551@N', ':552@N'].
> # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion
> No Rex - relax_disp 14 175 458.66116 486.66116
> CR72 - relax_disp 23 175 117.29418 163.29418
> The model from the data pipe 'CR72 - relax_disp' has been selected.
> ———
This looks reasonable. This is 7 spins, so on average, 117.29/7 =
16.76, which is a little more than the single spin value of 13.94.
> But there is no corresponding data table.
Do you mean that there is no ‘disp_530_N.out’ file for the clustered analysis?
> ###########
>
> QUESTION 1:
> Is it possible to get, or easily create a table with, in my case, 175 R2eff_(back_calc) for the cluster, so that I can get better resolution on the Chi2 = 117.29418 above ?
> And possibly study how a single residue affect the cluster fitting.
Try the value.write() user function:
https://www.nmr-relax.com/manual/value_write.html
Make sure to set the 'bc' flag to True.
> QUESTION 2:
> Are there any reference to methods used for doing efficient selection of residues included in the cluster? There is obviously an immense number of combinations of residues to make clusters in a normal size protein. I consider making a program/script for this process and would be curious to get some inspiration.
As far as I am aware, human logic is used for this process. You
identify a rigid moving unit in your system yourself with similar
dispersion results and then use clustering on that. I would assume
that an automated system to find clusters would be computationally
very expensive, despite being able to run on a computer cluster via
MPI. And that such a project would take up half or more of a PhD
student's time. Then again, I wouldn't be surprised if there is now a
publication exploring this concept. If you do find one, I'd be
interested in hearing about it.
Regards,
Edward
|
|
From: Johan W. <joh...@gu...> - 2022-06-29 11:12:05
|
Hi, I perform CPMG-RD cluster fitting using relax, cluster refer to grouping several residues (between 3 to 14 residues) for data from a 45 kDa protein. The software is a good tool for doing this analysis. I marginally adjust the core protocol with the header """Script for performing a full relaxation dispersion analysis using CPMG-type data.""" I use only the CR72-model and I have a PRE_RUN_DIR from a run with individual residues. I use duplicates for error estimation, on both the 800 MHz and 900 MHz data set, and AIC for model selection. When I analyse the clustered data I’m curious to get R2eff_(back_calc) for each data point. I clarify my main question by attaching some of my data. ########### For residue 530, when I do individual fit I get this output. From the log-file: ——— The spin cluster [':530@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 2 25 21.11216 25.11216 CR72 - relax_disp 5 25 13.93686 23.93686 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— The file ‘disp_530_N.out’ in /final gives the following data table: # Experiment_name Field_strength_(MHz) Disp_point_(Hz) R2eff_(measured) R2eff_(back_calc) R2eff_errors 'SQ CPMG' 799.870000000 25.000000 17.523783179912268 16.953711340740483 0.831932502443187 'SQ CPMG' 799.870000000 50.000000 16.513029763549930 16.914478241596726 0.805586049587058 'SQ CPMG' 799.870000000 75.000000 16.920353186819355 16.875245142453196 0.816049323427317 'SQ CPMG' 799.870000000 100.000000 16.667402888129434 16.836012043882192 0.809527349094067 'SQ CPMG' 799.870000000 150.000000 16.454146002323920 16.757546676539960 0.804090431533660 'SQ CPMG' 799.870000000 200.000000 16.359623786385509 16.679111600438773 0.801698521274394 'SQ CPMG' 799.870000000 300.000000 15.525257427659495 16.523477804972345 0.781054888748662 'SQ CPMG' 799.870000000 350.000000 16.609858567997016 16.447662190184474 0.808054742944598 'SQ CPMG' 799.870000000 400.000000 16.844330710216166 16.374401478154368 0.814080812205130 'SQ CPMG' 799.870000000 500.000000 17.414128601521103 16.238705811895670 0.829011905615397 'SQ CPMG' 799.870000000 600.000000 16.093980388806685 16.120475644003818 0.795034804815920 'SQ CPMG' 799.870000000 800.000000 15.988036247232372 15.937187687218284 0.792401090807446 'SQ CPMG' 799.870000000 1000.000000 15.732649459437805 15.811741022120714 0.786107934589661 'SQ CPMG' 900.130000000 57.000000 19.386713898811351 20.163621643615215 0.801212497068354 'SQ CPMG' 900.130000000 114.000000 21.873502893081564 20.050473540803750 0.859660006101508 'SQ CPMG' 900.130000000 171.000000 19.133628964210569 19.937331394199191 0.795598311646227 'SQ CPMG' 900.130000000 228.000000 20.497316023709256 19.824330722189416 0.826567798566107 'SQ CPMG' 900.130000000 285.000000 20.091262254550443 19.712140304427066 0.817160298225920 'SQ CPMG' 900.130000000 400.000000 19.177817248045365 19.494278567900892 0.796574222459005 'SQ CPMG' 900.130000000 514.000000 19.111643299707755 19.300194513689348 0.795113430566997 'SQ CPMG' 900.130000000 628.000000 18.432363807026835 19.135138271300775 0.780352695478047 'SQ CPMG' 900.130000000 742.000000 19.383070346051138 18.999531230125285 0.801131245976946 'SQ CPMG' 900.130000000 857.000000 18.560791856291317 18.889165645990943 0.783110910382522 'SQ CPMG' 900.130000000 971.000000 18.810639108776328 18.801416118812085 0.788520121686263 'SQ CPMG' 900.130000000 1085.000000 18.943973311789268 18.730884832131551 0.791430360141496 ########### For a cluster fit (including residue 530) I get this output from the log-file: ——— The spin cluster [':530@N', ':536@N', ':537@N', ':538@N', ':550@N', ':551@N', ':552@N']. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion No Rex - relax_disp 14 175 458.66116 486.66116 CR72 - relax_disp 23 175 117.29418 163.29418 The model from the data pipe 'CR72 - relax_disp' has been selected. ——— But there is no corresponding data table. ########### QUESTION 1: Is it possible to get, or easily create a table with, in my case, 175 R2eff_(back_calc) for the cluster, so that I can get better resolution on the Chi2 = 117.29418 above ? And possibly study how a single residue affect the cluster fitting. QUESTION 2: Are there any reference to methods used for doing efficient selection of residues included in the cluster? There is obviously an immense number of combinations of residues to make clusters in a normal size protein. I consider making a program/script for this process and would be curious to get some inspiration. Best regards Johan Wallerstein, Sweden |
|
From: Hendrik K. <hen...@ru...> - 2022-02-22 12:34:38
|
Dear all,
at first I would like to thank all of you for your fast responses! I
really appreciate your assistance and I am really thankful that there is
such a helpful and respectful NMR community out there!
I did not respond earlier to your previous messages, as I wanted to make
sure to not ran into another problem. I could figure out the reason for
the error of my previous described problem. The error with the error
message:
relax>
spectrum.read_intensities(file='/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms',
dir=None, spectrum_id='5', dim=1, int_method='height', int_col=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, ncproc=None)
Opening the file
'/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms'
for reading.
Sparky formatted data file.
Number of header lines found: 1
2D peak list detected.
Traceback (most recent call last):
File "/usr/software/relax/gui/interpreter.py", line 109, in apply
fn(*args, **kwds)
File "/usr/software/relax/pipe_control/spectrum.py", line 610, in
read
peak_list = read_peak_list(file=file[file_index], dir=dir,
int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id)
File "/usr/software/relax/lib/spectrum/peak_list.py", line 213,
in read_peak_list
sparky.read_list(peak_list=peak_list, file_data=file_data)
File "/usr/software/relax/lib/spectrum/sparky.py", line 127, in
read_list
name2 = row2[-2] + row2[-1]
IndexError: list index out of range
was caused by a question mark character in my peak list, which
originated in an unassigned nitrogen dimension of a residue in my CCPNMR
project:
Assignment w1 w2 Height
F142H-? 8.684 119.044 8.09E+04
So i could fix that problem by assign it and generate new peak lists for
my spectra and go on with the R1, R2 and NOE analysis without any
further issues. Then I tried to go on with a model free analysis. I
loaded the spins for protons and nitrogen from my previous described
sequence file and added the "element" attribute for each spin by hand.
When I tried to prepare the dipole-dipole interactions I came across
another error message which says:
relax>interatom.unit_vectors(ave=True)
Averaging all vectors.
RelaxError: Positional information could not be found for any spins.
I found an entry in the mailing list archive, where another user had
this issue
(https://www.mail-archive.com/rel...@gn.../msg01491.html). Is it
right, that I have to use a 3D structure instead of a sequence file for
the model free analysis, as only this will provide the necessary
positional information or did I do something wrong with loading my
sequence file?
Best regards and thanks for your help!
Hendrik
Am 16.02.22 um 23:55 schrieb Edward d'Auvergne:
> On Wed, 16 Feb 2022 at 19:25, Hendrik Kirschner via nmr-relax-users
> <nmr...@li...> wrote:
>> Dear all,
>>
>> I am new to Relax and wanted to analyze my relaxation data with it. I used CCPNMR V2.4.2 to export my peak lists from my T1, T2 and NOE data sets in sparky format. Also the sequence file was generated with CCPNMR V2.4.2. Then i started the analysis with relax 5.0.0 at NMRbox.org. The loading of the spins from the sequence file was successfull and spin container for all residues were generated with H and N spins in it each.
>>
>> My sequence file is formatted like this:
>>
>> res_num res_name spin_num spin_name
>> -2 Gly -2 N
>> -1 His -1 N
>> 0 Met 0 N
>> 1 Ser 1 N
>>
>> But when i tried to load my relaxation data ("peak intensity reading" window) i always get the following error message:
>>
>> relax> spectrum.read_intensities(file='/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms', dir=None, spectrum_id='5', dim=1, int_method='height', int_col=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, ncproc=None)
>> Opening the file '/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms' for reading.
>> Sparky formatted data file.
>>
>> Number of header lines found: 1
>> 2D peak list detected.
>>
>> Traceback (most recent call last):
>> File "/usr/software/relax/gui/interpreter.py", line 109, in apply
>> fn(*args, **kwds)
>> File "/usr/software/relax/pipe_control/spectrum.py", line 610, in read
>> peak_list = read_peak_list(file=file[file_index], dir=dir, int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
>> File "/usr/software/relax/lib/spectrum/peak_list.py", line 213, in read_peak_list
>> sparky.read_list(peak_list=peak_list, file_data=file_data)
>> File "/usr/software/relax/lib/spectrum/sparky.py", line 127, in read_list
>> name2 = row2[-2] + row2[-1]
>> IndexError: list index out of range
>>
>> The sparky format of the data looks like this:
>>
>> Assignment w1 w2 Height
>> K18H-K18N 8.134 123.117 6.63E+05
>>
>>
>> I tried different settings in the "peak intensity reading" window (e.g. intensity column set to 3 or 4). I also searched in the mailing list and Wiki for a solution and found an entry which seems to describe my problem (-> bug #22961; found at:http://wiki.nmr-relax.com/Relax_release_bugfixes), but the description does not really helped me. I also tried a different Relax version (V4.1.3) and to load the spins via a PDB-file, but it leads to the same error.
>>
>> Is there anything wrong with my formats or did I do something wrong in the settings?
> Hi Hendrik,
>
> Welcome to the relax mailing lists! That is an interesting problem
> that I don't think anyone has encountered before. I wonder if it is
> due to CCPN not producing a conformant Sparky formatted file. For the
> example you gave, I can see that the 'K18H-K18N' assignment works ok.
> Using the python3 interpreter and replicating the failing lines of
> code:
>
>>>> from re import split
>>>> assign2 = "K18N"
>>>> row2 = split('([a-zA-Z]+)', assign2)
>>>> row2[-2] + row2[-1]
> 'N'
>
> relax correctly finds 'N' for the name of the 2nd dimension. What you
> could do is to randomly delete blocks of lines from your
> Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms file, running relax
> to find which line is causing the error. You should be able to repeat
> this until you only have a single failing line left. If you could
> find that line and report it back, that would be appreciated. I can
> then see if it is something that should be fixed in relax or in the
> CCPN Sparky export.
>
> Cheers,
>
> Edward
--
Hendrik Kirschner, M.Sc.
Biomolecular NMR (NC5/173 Süd)
Faculty of Chemistry and Biochemistry
Ruhr-University Bochum
Universitaetsstrasse 150
44801 Bochum
Germany
Hen...@ru...
Tel.: +49 234 32-26246
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From: Mark B. <mar...@tu...> - 2022-02-18 21:44:03
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Dear Edward,
I used CCPN for my spectra and exported a CCPN peak list, which contains
all relaxation planes and peaks in the same file (my data is acquired as
a pseudo 3D). I wrote a python converter, which writes out sparky format
peak lists and the sequence file. I then use these for the input to relax.
Best wishes,
Mark
On 16/02/2022 23:00, Edward d'Auvergne wrote:
> On Wed, 16 Feb 2022 at 23:19, Mark Bostock <mar...@tu...> wrote:
>> Dear Hendrik,
>>
>> I have not used Relax for T1/T2/NOE data (I assume you are planning to do model-free analysis). However, for CPMG analysis I have the following formats for my input files:
>>
>> Peak intensity files:
>>
>> Assignment w1 w2 Data Height
>> ASP2N-HN 8.560 122.651 2.98553e+08
>> SER3N-HN 8.425 116.521 2.47809e+08
>> THR4N-HN 8.358 115.634 2.42621e+08
>> SER5N-HN 8.264 117.706 2.65439e+08
>>
>> Sequence file (no headers):
>>
>> 2 Asp
>> 3 Ser
>> 4 Thr
>> 5 Ser
>>
>> In the relax script this is loaded as:
>>
>> # Load the sequence.
>> sequence.read('sequence.txt', dir=DATA_PATH, res_num_col=1, res_name_col=2)
>>
>> I hope this helps. The sequence file format seems to be quite different. The variable number of spaces between your first and second columns may cause problems.
> Hi Mark,
>
> Thanks for replying! Did you use Sparky directly or CCPN export as
> well? Maybe it is time to add support for CCPN peak lists. Note that
> after 2 decades and hundreds of relax users throwing all sorts of data
> at it, the handling of different file formats and conventions by relax
> is now no problem at all and is mostly automated. The relax design
> philosophy is that the user is never wrong, or never has incorrectly
> formatted data ;) In the later case, a carefully crafted RelaxError
> message is used to fully explain the issue.
>
> Cheers,
>
> Edward
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From: Edward d'A. <ed...@nm...> - 2022-02-16 23:01:06
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On Wed, 16 Feb 2022 at 23:19, Mark Bostock <mar...@tu...> wrote:
>
> Dear Hendrik,
>
> I have not used Relax for T1/T2/NOE data (I assume you are planning to do model-free analysis). However, for CPMG analysis I have the following formats for my input files:
>
> Peak intensity files:
>
> Assignment w1 w2 Data Height
> ASP2N-HN 8.560 122.651 2.98553e+08
> SER3N-HN 8.425 116.521 2.47809e+08
> THR4N-HN 8.358 115.634 2.42621e+08
> SER5N-HN 8.264 117.706 2.65439e+08
>
> Sequence file (no headers):
>
> 2 Asp
> 3 Ser
> 4 Thr
> 5 Ser
>
> In the relax script this is loaded as:
>
> # Load the sequence.
> sequence.read('sequence.txt', dir=DATA_PATH, res_num_col=1, res_name_col=2)
>
> I hope this helps. The sequence file format seems to be quite different. The variable number of spaces between your first and second columns may cause problems.
Hi Mark,
Thanks for replying! Did you use Sparky directly or CCPN export as
well? Maybe it is time to add support for CCPN peak lists. Note that
after 2 decades and hundreds of relax users throwing all sorts of data
at it, the handling of different file formats and conventions by relax
is now no problem at all and is mostly automated. The relax design
philosophy is that the user is never wrong, or never has incorrectly
formatted data ;) In the later case, a carefully crafted RelaxError
message is used to fully explain the issue.
Cheers,
Edward
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From: Edward d'A. <ed...@nm...> - 2022-02-16 22:55:19
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On Wed, 16 Feb 2022 at 19:25, Hendrik Kirschner via nmr-relax-users <nmr...@li...> wrote: > > Dear all, > > I am new to Relax and wanted to analyze my relaxation data with it. I used CCPNMR V2.4.2 to export my peak lists from my T1, T2 and NOE data sets in sparky format. Also the sequence file was generated with CCPNMR V2.4.2. Then i started the analysis with relax 5.0.0 at NMRbox.org. The loading of the spins from the sequence file was successfull and spin container for all residues were generated with H and N spins in it each. > > My sequence file is formatted like this: > > res_num res_name spin_num spin_name > -2 Gly -2 N > -1 His -1 N > 0 Met 0 N > 1 Ser 1 N > > But when i tried to load my relaxation data ("peak intensity reading" window) i always get the following error message: > > relax> spectrum.read_intensities(file='/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms', dir=None, spectrum_id='5', dim=1, int_method='height', int_col=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, ncproc=None) > Opening the file '/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms' for reading. > Sparky formatted data file. > > Number of header lines found: 1 > 2D peak list detected. > > Traceback (most recent call last): > File "/usr/software/relax/gui/interpreter.py", line 109, in apply > fn(*args, **kwds) > File "/usr/software/relax/pipe_control/spectrum.py", line 610, in read > peak_list = read_peak_list(file=file[file_index], dir=dir, int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id) > File "/usr/software/relax/lib/spectrum/peak_list.py", line 213, in read_peak_list > sparky.read_list(peak_list=peak_list, file_data=file_data) > File "/usr/software/relax/lib/spectrum/sparky.py", line 127, in read_list > name2 = row2[-2] + row2[-1] > IndexError: list index out of range > > The sparky format of the data looks like this: > > Assignment w1 w2 Height > K18H-K18N 8.134 123.117 6.63E+05 > > > I tried different settings in the "peak intensity reading" window (e.g. intensity column set to 3 or 4). I also searched in the mailing list and Wiki for a solution and found an entry which seems to describe my problem (-> bug #22961; found at: http://wiki.nmr-relax.com/Relax_release_bugfixes), but the description does not really helped me. I also tried a different Relax version (V4.1.3) and to load the spins via a PDB-file, but it leads to the same error. > > Is there anything wrong with my formats or did I do something wrong in the settings? Hi Hendrik, Welcome to the relax mailing lists! That is an interesting problem that I don't think anyone has encountered before. I wonder if it is due to CCPN not producing a conformant Sparky formatted file. For the example you gave, I can see that the 'K18H-K18N' assignment works ok. Using the python3 interpreter and replicating the failing lines of code: >>> from re import split >>> assign2 = "K18N" >>> row2 = split('([a-zA-Z]+)', assign2) >>> row2[-2] + row2[-1] 'N' relax correctly finds 'N' for the name of the 2nd dimension. What you could do is to randomly delete blocks of lines from your Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms file, running relax to find which line is causing the error. You should be able to repeat this until you only have a single failing line left. If you could find that line and report it back, that would be appreciated. I can then see if it is something that should be fixed in relax or in the CCPN Sparky export. Cheers, Edward |
