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 (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
