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 and would appreciate if you >> have a look. >> >> Thank you. >> Olena >> >> >> ________________________________________ >> From: Stefano Luciano Ciurli >> Sent: 10 June 2014 13:39 >> To: Edward d'Auvergne >> Cc: relax-users@gna.org; Olena Dobrovolska >> Subject: Re: dimer >> >> Hi Edward, >> 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. >> 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. >> Looking forward to hearing from you >> Stefano >> >> On Jun 6, 2014, at 8:35 AM, Edward d'Auvergne wrote: >> >>> 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 >>> TER 2441 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 >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@gna.org >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
