From: Yang M. <jef...@16...> - 2007-10-24 13:33:34
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Dear all, A new user to pymol. I have a question about the superposition of two molecules. To say it clearly, for example, there are two structures of a molecule in two pdb files, one including 20-200 residues, the other including 10-180 residues, where the structures of shared residues 10-180 are almost the same. What I want to do is to incorporate the coordinate information in one pdb file(containing residues 10-180, in which the residues 10-19 are missed in the other file) into the other one, which includes residues 20-200. The final result is a pdb file containing residues 10-200, with a correct connected bond and orientation between residue 19 and 20. The coordinates of residues 20-180 are almost the same but not exact. I am wondering whether PyMol can solve this question exact and how. Any suggestion is greatly appreciated. Thanks. ------ Jeff |
From: DeLano S. <de...@de...> - 2007-10-25 16:17:56
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Jeff, PyMOL isn't a homology modeling tool, but in combination with something like GROMACS, you might able to accomplish something like this. Although one can easily use PyMOL to graft and assemble molecules, that last step of cleaning up the "joints" and any missing residues requires an external minimization. Here is an example of coordinate grafting: # load HIV protease (symmetric dimer) load $TUT/1hpv.pdb # map chain A coordinates onto chain B coord_dict = {} iterate_state 1, chain A, coord_dict[(resi,name)]=(x,y,z) alter_state 1, chain B, (x,y,z)=coord_dict.get((resi,name),(x,y,z)) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@de... to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Yang Mingjun > Sent: Wednesday, October 24, 2007 6:33 AM > To: pymol-users > Subject: [PyMOL] Superposition and connect of two segment > > Dear all, > A new user to pymol. > I have a question about the superposition of two > molecules. To say it clearly, for example, there are two > structures of a molecule in two pdb files, one including > 20-200 residues, the other including 10-180 residues, where > the structures of shared residues 10-180 are almost the same. > What I want to do is to incorporate the coordinate > information in one pdb file(containing residues 10-180, in > which the residues 10-19 are missed in the other file) into > the other one, which includes residues 20-200. The final > result is a pdb file containing residues 10-200, with a > correct connected bond and orientation between residue 19 and > 20. The coordinates of residues 20-180 are almost the same > but not exact. > > I am wondering whether PyMol can solve this question exact and how. > Any suggestion is greatly appreciated. > > Thanks. > > ------ > Jeff > > > > |