Hi Jacob, * Jacob Corn <jc...@uclink.berkeley.edu> [2005-04-15 09:28] wrote: > Hi Robert, > You're exactly right. It's a chainid issue. If I load 2 PDBs with > different chainids, they "merge" without a problem. If they have a the > same chainid, lines display OK, but the sequence viewer and > ribbons/cartoon view makes the problem clear. > > As background, what we were trying to do was use PyMOL as to model > multimers from several different monomers, using distantly related > structures as a template, and then create a composite model from the > monomers and it as one PDB. Basically just trying to save time, rather > than writing out several rotated/translated monomer PDBs and collating them. > > I don't know about anyone else, but I think that task would be nice to > do in PyMOL. Would it be hard to alter the create command so that it > makes sure there are no clashes between atom/chain/etc. naming?
For your multimers can you not simply alter the chain ids with the alter command? For a trimer: alter object2, chain='B' alter object3, chain='C' create merged, object1 | object2 | object3 Or if you want to keep the same chain id for all, then you would need to renumber before merging (e.g. to add 123 to each residue number): alter object2, resi=str(int(resi)+123) Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
