Re: [PyMOL] mapping atom names between molecules

[Thomas H. <sp...@us...>]

Hi Sean,

if you want to do mapping by alignment, all PyMOL alignment commands 
support an "object" argument which creates an alignment object.

See the example on this PyMOLWiki page: 
http://pymolwiki.org/index.php/Get_raw_alignment

Note that for cealign the support for the object argument got added very 
recently to open-source PyMOL.

You may also be interested in the psico.fitting.MatchMaker class, which 
provides matched atom selections. Example:

from psico.fitting import MatchMaker
mm = MatchMaker('mol1', 'mol2', 'align')
cmd.iterate(mm.mobile, 'print (model,chain,resi,resn,name)')
cmd.iterate(mm.target, 'print (model,chain,resi,resn,name)')

Cheers,
   Thomas

Sean Law wrote, On 08/16/12 15:16:
> I too have encountered a similar problem and was hoping that somebody 
> had a suggestion for this.  I've tried using CEALIGN to attempt to align 
> the molecules and then hoped that I could simply use some atom-atom 
> pairwise distances to map one set of atoms onto another but CEALIGN 
> doesn't seem to work for non-standard atom names?
> 
> Any help would be greatly appreciated.
> 
> Thanks!

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen