RE: dimer
Hi Edward, Yes, I solved this problem manually that day, i.e.I have started the calculations. The problem was that I cut the DC files into the parts I was interested, which caused the change of the format somehow. So I had to manually (omparing to the original file) make sure that the spaces between the lines were identical. However, it has been running and already more than a week at the 'oblate' stage. Is it normal? Or perhaps again there is inconsistency with the fact that I run it on the virtual machine Xubuntu installed on Windows platform? We will instal Relax on the new computer on Linux and then I will run once again and see if the situation will change. Thanks for your prompt reply and a hint where to look. Regards, Olena From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 18 August 2014 08:39 To: Troels Emtekær Linnet Cc: Olena Dobrovolska; Stefano Luciano Ciurli; relax-users@gna.org Subject: Re: dimer Hi Olena, I hope you have already solved this problem. I have just returned from holidays, hence the late reply. You will need to either obtain the latest relax sources as I haven't released a new relax version yet (see http://www.nmr-relax.com/download.html#Source_code_repository) or manually delete the spaces on all empty lines in all your files. I have not done this myself, as I have modified relax to handle the spaces. I do not know why there are spaces in your Bruker DC files, as none of the reference files Bruker sent me as we were collaboratively developing the relax-Bruker DC compatibility interface contained spaces (as can be found on the relax development mailing list, search for Neidig at http://dir.gmane.org/gmane.science.nmr.relax.devel). So either this has been introduced in a newer Topspin version or Bruker DC file version or by some other means. Regards, Edward On 31 July 2014 18:49, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: Dear Olena. If it has any interest, I just wish to turn your attention into, that it is possible to run relax on both Windows and Mac. I made these guide, when I tried a MS system, http://wiki.nmr-relax.com/Installation_windows_Python_x86-32_Visual_Studio_Express_for_Windows_Desktop And for mac. http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x Best Troels 2014-07-31 17:27 GMT+02:00 Olena Dobrovolska olena.dobrovol...@unibo.it: Dear Edward, I have doubled the spins for the NOE, T1, T2 files to run the analysis for the dimer. The analysis took more than a month, and it was not completed (stopped at the 'prolate' step), I believe because we were running it on a virtual machine (Xubuntu), and not on a Linux computer, which we are going to do. However, I wanted also to try running Relax on the separate protein parts. The protein we are working with is composed of the domains arranged as N-C-C-N. And I would like to run the first calculation for the C-C part, for which I prepared the NOE, T1 and T2 files (output from DC) by doubling the spins and cutting off the N-terminal parts (in the same way I have prepared also the data for the N-terminal domain of the protein). However, I can not load the data and therefore start the calculations. Whereas the NOE files loading went well, for the T1 or T2 files upload Relax gives me the following error message: relax bruker.read(ri_id='T1_700_N', file='/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt', dir=None) Opening the file '/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt' for reading. Traceback (most recent call last): File /usr/local/relax-3.2.1/gui/wizards/wiz_objects.py, line 670, in _go_next self._pages[self._current_page]._apply(event) File /usr/local/relax-3.2.1/gui/wizards/wiz_objects.py, line 164, in _apply self.exec_status = self.on_execute() File /usr/local/relax-3.2.1/gui/uf_objects.py, line 887, in on_execute return_status = self.execute(self.name, **kargs) File /usr/local/relax-3.2.1/gui/uf_objects.py, line 809, in execute return_status = interpreter.apply(uf, *args, **kwds) File /usr/local/relax-3.2.1/gui/interpreter.py, line 109, in apply apply(fn, args, kwds) File /usr/local/relax-3.2.1/pipe_control/bruker.py, line 54, in read values, errors, res_nums, int_type, frq, ri_type, spin_name, isotope, version = parse_file(file=file, dir=dir) File /usr/local/relax-3.2.1/lib/software/bruker_dc.py, line 164, in parse_file rx = float(row[-2]) IndexError: list index out of range Therefore, I couldn't even load the dataset for this protein part, or precisely the T1 and T2 data. The files format is identical to those used for the full protein. Why then it doesn't want to load? For me it is unclear in this message where could be the problem. Could you please help? If you want I can send you only the files I prepared
Re: dimer
Hi Olena, The time it takes for optimisation depends directly on the complexity of motion in your system, the quality of the XH bond vector orientations, the quality of your data (have you tried Sebastien Morin's consistency testing analysis?), and how well the approximation of a single, simple diffusion tensor is for your system. These can affect the total number of iterations of the protocol which can vary between 2 and the maximum which defaults to 30. Also the speed of the computer can have a large effect. And having access to a cluster and using Gary Thompson's multi-processor and OpenMPI will have a huge effect on your calculation time. The virtual machine may also have a large effect. The time could be between a few minutes on a massive cluster with a rigid protein system to a few weeks on the slowest system with complex dynamics and non-standard Brownian diffusion. But there are just too many factors involved to know. As Troels mentioned, you can run this directly on Windows. It is rather easy to set up a Python environment for relax on Windows and I don't think you even need to be an administrator on certain systems. This will probably give you more speed. Regards, Edward On 18 August 2014 11:30, Olena Dobrovolska olena.dobrovol...@unibo.it wrote: Hi Edward, Yes, I solved this problem manually that day, i.e.I have started the calculations. The problem was that I cut the DC files into the parts I was interested, which caused the change of the format somehow. So I had to manually (omparing to the original file) make sure that the spaces between the lines were identical. However, it has been running and already more than a week at the 'oblate' stage. Is it normal? Or perhaps again there is inconsistency with the fact that I run it on the virtual machine Xubuntu installed on Windows platform? We will instal Relax on the new computer on Linux and then I will run once again and see if the situation will change. Thanks for your prompt reply and a hint where to look. Regards, Olena From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of Edward d'Auvergne [edw...@nmr-relax.com] Sent: 18 August 2014 08:39 To: Troels Emtekær Linnet Cc: Olena Dobrovolska; Stefano Luciano Ciurli; relax-users@gna.org Subject: Re: dimer Hi Olena, I hope you have already solved this problem. I have just returned from holidays, hence the late reply. You will need to either obtain the latest relax sources as I haven't released a new relax version yet (see http://www.nmr-relax.com/download.html#Source_code_repository) or manually delete the spaces on all empty lines in all your files. I have not done this myself, as I have modified relax to handle the spaces. I do not know why there are spaces in your Bruker DC files, as none of the reference files Bruker sent me as we were collaboratively developing the relax-Bruker DC compatibility interface contained spaces (as can be found on the relax development mailing list, search for Neidig at http://dir.gmane.org/gmane.science.nmr.relax.devel). So either this has been introduced in a newer Topspin version or Bruker DC file version or by some other means. Regards, Edward On 31 July 2014 18:49, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: Dear Olena. If it has any interest, I just wish to turn your attention into, that it is possible to run relax on both Windows and Mac. I made these guide, when I tried a MS system, http://wiki.nmr-relax.com/Installation_windows_Python_x86-32_Visual_Studio_Express_for_Windows_Desktop And for mac. http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x Best Troels 2014-07-31 17:27 GMT+02:00 Olena Dobrovolska olena.dobrovol...@unibo.it: Dear Edward, I have doubled the spins for the NOE, T1, T2 files to run the analysis for the dimer. The analysis took more than a month, and it was not completed (stopped at the 'prolate' step), I believe because we were running it on a virtual machine (Xubuntu), and not on a Linux computer, which we are going to do. However, I wanted also to try running Relax on the separate protein parts. The protein we are working with is composed of the domains arranged as N-C-C-N. And I would like to run the first calculation for the C-C part, for which I prepared the NOE, T1 and T2 files (output from DC) by doubling the spins and cutting off the N-terminal parts (in the same way I have prepared also the data for the N-terminal domain of the protein). However, I can not load the data and therefore start the calculations. Whereas the NOE files loading went well, for the T1 or T2 files upload Relax gives me the following error message: relax bruker.read(ri_id='T1_700_N', file='/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt', dir=None) Opening the file '/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt' for reading. Traceback
Re: dimer
Hi Stefano,
For what has happened here, you need to open up your log file. Did
you use relax with the --log or --tee command line options to capture
the messages? If you go to the start of the messages, you will very
likely find RelaxWarnings which say something like deselecting the
spin due to missing {relaxation data; bond vector information; etc.}
or due to something else in the set up. In relax, everything that
happens is sent to the log so you can always go back and see exactly
what happened. I hope this solves your problem.
Regards,
Edward
On 10 June 2014 23:53, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
Hi Edward, an additional question: in the output file I noticed that the last
four residues at the C-terminus, for which I provided relaxation data, are
not included. Any reason for it? (for the previous 9 residues we did not have
the assignment because they are not observed due to intermediate exchange
phenomena that broaden them too much to be visible, while the last four
residues are clearly visible and they appear to be very mobile, and yet, no
output from relax.
Stefano
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Re: dimer
Hi Stefano, It will be interesting to see the results in your final publication. well, same for us of course. However, this is the first time I approach this problem, so I welcome any advice. Especially considering that the relaxation data you observe is the average of two states experiencing different global tumbling (the two vectors intersect different parts of a single Brownian diffusion tensor), but the assumption is made that they only sample one. the dimer is perfectly symmetric in solution, in the NMR time scale, as we observe only a single peak per residue For dimers, unfortunately I don't have much advice I can give. The only person who could we be the one who derives the correct theoretical treatment of dimers in the future. You may have avoided the issue though if you have a perfectly symmetrical dimer. Maybe you should perform a full analysis on one monomer, and then another full analysis on the second, and compare. I am not sure that I understand your suggestion, as the two monomers are inextricably bound It won't give much, but the bond vectors orientations are different between two monomers. The superimposition is not perfect. But, as we have discussed before on the list, it will not do anything for the theoretical problem, if you indeed do have a problem. It will only show you any small bond vector orientation artefacts. Are you sure there are no published theoretical treatments of such a situation? I am aware of relaxation studies on homodimeric proteins, but I am also quite sure that the papers do not tackle the issue of the dimer and report the relaxation data as for a monomeric protein; again, any advice is welcome. I am also unaware of any theoretical treatment. If you deposit your dynamics data for your publication in the BMRB, via the relax export functions, then this might open a door to allow a theoretician in the future to use real data for solving this problem. As for solving the problem now and you are 100% sure that this is not already solved, unless you would like to dive into quite complex theory, then there is nothing we can do. You could make a 1 line comment about the deficiency in the manuscript, and make the statement that this is an unsolved problem. Anyway, the perfect symmetry might mean that the diffusion tensor as seen in the reference frame of each monomer is identical, so that the bond vectors in each experience the same 5 global correlation times and hence the standard analysis will work perfectly. If so, no special theory is required. Regards, Edward ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: dimer
Hi Stefano, Please see below: thinking about it, and considering that we erroneously run Relax using the full PDB for the homodimer but provided only the T1, T2 and NOE data for one monomer, as output of Dynamics Center, could you tell us how to modify the .txt files from Dynamics Center so that Relax thinks it has a full set of data for the full homodimer? The PDB that we used has residues already numbered consecutively from residue 1 to the last residue of the dimer. In this setup, relax will only look at the first monomer. We really need to change the input files for T1, T2 and NOE in order to decide which part of the protein we are looking at, but we would like to know which parts of the output files from DC should be duplicated. If you want and need it, I can send you the files in a private email to you only. There is no need to send the files. Do you have someone there who knows scripting? One option is to write a script (perl, Python, sed, etc.) which adds 147 to the residue number for all parts of the Bruker DC file. Or maybe using the script at http://thread.gmane.org/gmane.science.nmr.relax.user/1661/focus=1677 to renumber the PDB file will be sufficient. Loading the two molecules into relax and then loading the Bruker DC data might put the data into the spin containers of both molecules, as the residue numbers for both molecules will match. This would have to be very carefully checked as this is completely untested behaviour for relax. You would also need to carefully look at the log messages. If you would like me to make this last option 100% functional for relax, I would recommend creating a support request and attaching your Bruker DC files there - but they must be truncated to 1 or 2 residues. You can randomise the data slightly too for complete secrecy, if you wish. I could then use this and the PDB file to create a relax system test. Having a system test allows me to fix things in relax in ~5 to 10 minutes. The support request creation link is http://gna.org/support/?func=additemgroup=relax. Regards, Edward ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: dimer
Hi Edward, an additional question: in the output file I noticed that the last four residues at the C-terminus, for which I provided relaxation data, are not included. Any reason for it? (for the previous 9 residues we did not have the assignment because they are not observed due to intermediate exchange phenomena that broaden them too much to be visible, while the last four residues are clearly visible and they appear to be very mobile, and yet, no output from relax. Stefano ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: dimer
Hi Stefano,
It will be interesting to see the results in your final publication.
Especially considering that the relaxation data you observe is the
average of two states experiencing different global tumbling (the two
vectors intersect different parts of a single Brownian diffusion
tensor), but the assumption is made that they only sample one. Maybe
you should perform a full analysis on one monomer, and then another
full analysis on the second, and compare. Are you sure there are no
published theoretical treatments of such a situation?
As for the PyMOL or MOLMOL macros, I've had a look at the PDB file you
attached to http://gna.org/support/?3110, and this might be difficult.
Although both molecules are represented as different chains, the
residue numbers are not reset between the A to B transition:
ATOM 2437 HE1 HIS A 147 14.544 -14.592 44.384 1.00142.09 H
ATOM 2438 C HIS A 147 15.448 -12.825 50.108 1.00142.09 C
ATOM 2439 O HIS A 147 16.622 -12.826 50.563 1.00142.09 O
ATOM 2440 OXT HIS A 147 14.601 -13.730 50.336 1.00142.09 O
TER2441 HIS A 147
ATOM 2442 N MET B 148 34.965 4.924 102.588 1.00 83.68 N
ATOM 2443 H MET B 148 35.604 5.224 103.352 1.00 83.68 H
ATOM 2444 CA MET B 148 33.567 5.117 103.004 1.00 83.68 C
Do you have the ability to renumber residues? This is rather simple
in relax, though not so obvious as it plays directly with the relax
data store object and uses Python programming:
# Create a data pipe.
pipe.create('renumber', 'N-state')
# Load the original PDB as two molecules.
structure.read_pdb('BpUreE_apo_model_full.pdb')
# Renumber all residues of the second molecule directly in the
internal structural object.
for i in range(len(cdp.structure.structural_data[0].mol[1].res_num)):
cdp.structure.structural_data[0].mol[1].res_num[i] -= 147
# Write out the renumbered structure as a PDB file.
structure.write_pdb('BpUreE_apo_renumbered.pdb', force=True)
If the residues are all the same, then the PyMOL or MOLMOL macros
should apply to both structures. I just had a look and the macros
from the model-free analysis apply to residue numbers:
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.pymol-pysrc.html#Pymol.classic_colour
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.molmol-pysrc.html#Molmol.classic_colour
Regards,
Edward
On 5 June 2014 23:32, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
Hi Edward,
I reached the end of the calculation of our protein dimer, and everything
went smooth. We used two fields, and tomorrow I am about to start collecting
the third field data. I wonder how to make it so that the molmol or pymol
macros used to visualize the various parameters along the protein backbone
can be twisted so that these are applied to both monomers instead of just one.
Cheers,
Stefano
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Re: dimer
Hello Edward,
It will be interesting to see the results in your final publication.
well, same for us of course. However, this is the first time I approach this
problem, so I welcome any advice.
Especially considering that the relaxation data you observe is the
average of two states experiencing different global tumbling (the two
vectors intersect different parts of a single Brownian diffusion
tensor), but the assumption is made that they only sample one.
the dimer is perfectly symmetric in solution, in the NMR time scale, as we
observe only a single peak per residue
Maybe
you should perform a full analysis on one monomer, and then another
full analysis on the second, and compare.
I am not sure that I understand your suggestion, as the two monomers are
inextricably bound
Are you sure there are no
published theoretical treatments of such a situation?
I am aware of relaxation studies on homodimeric proteins, but I am also quite
sure that the papers do not tackle the issue of the dimer and report the
relaxation data as for a monomeric protein; again, any advice is welcome.
As for the PyMOL or MOLMOL macros, I've had a look at the PDB file you
attached to http://gna.org/support/?3110, and this might be difficult.
Although both molecules are represented as different chains, the
residue numbers are not reset between the A to B transition:
ATOM 2437 HE1 HIS A 147 14.544 -14.592 44.384 1.00142.09 H
ATOM 2438 C HIS A 147 15.448 -12.825 50.108 1.00142.09 C
ATOM 2439 O HIS A 147 16.622 -12.826 50.563 1.00142.09 O
ATOM 2440 OXT HIS A 147 14.601 -13.730 50.336 1.00142.09 O
TER2441 HIS A 147
ATOM 2442 N MET B 148 34.965 4.924 102.588 1.00 83.68 N
ATOM 2443 H MET B 148 35.604 5.224 103.352 1.00 83.68 H
ATOM 2444 CA MET B 148 33.567 5.117 103.004 1.00 83.68 C
Do you have the ability to renumber residues?
of course I will look into your suggestion below.
I remain available for any advice you are able to provide. In the meantime, it
does not hurt collecting a third field...
Best regards,
Stefano
This is rather simple
in relax, though not so obvious as it plays directly with the relax
data store object and uses Python programming:
# Create a data pipe.
pipe.create('renumber', 'N-state')
# Load the original PDB as two molecules.
structure.read_pdb('BpUreE_apo_model_full.pdb')
# Renumber all residues of the second molecule directly in the
internal structural object.
for i in range(len(cdp.structure.structural_data[0].mol[1].res_num)):
cdp.structure.structural_data[0].mol[1].res_num[i] -= 147
# Write out the renumbered structure as a PDB file.
structure.write_pdb('BpUreE_apo_renumbered.pdb', force=True)
If the residues are all the same, then the PyMOL or MOLMOL macros
should apply to both structures. I just had a look and the macros
from the model-free analysis apply to residue numbers:
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.pymol-pysrc.html#Pymol.classic_colour
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.molmol-pysrc.html#Molmol.classic_colour
Regards,
Edward
On 5 June 2014 23:32, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
Hi Edward,
I reached the end of the calculation of our protein dimer, and everything
went smooth. We used two fields, and tomorrow I am about to start collecting
the third field data. I wonder how to make it so that the molmol or pymol
macros used to visualize the various parameters along the protein backbone
can be twisted so that these are applied to both monomers instead of just
one.
Cheers,
Stefano
___
relax (http://www.nmr-relax.com)
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reminder, or change your subscription options,
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