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 > 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? 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) 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
