Re: [PyMOL] Creating one object from two

[Robert C. <rl...@po...>]

Hi Jacob,

* Jacob Corn <jc...@uc...> [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.                         <rl...@po...>
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