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
