or if B' is residues M to N in prot1 and B'' is residues L to K in prot2, its as simple as

load prot1.pdb
load prot2.pdb

align prot1 and i. M-N, prot2 and i. L-K

look at "help selections" and you can try to align any two selections..

cheers,
Abhi.

On Thu, Mar 20, 2008 at 12:34 PM, DeLano Scientific <delsci@delsci.info> wrote:
Carlo,

If B is the chain ID for the matched seguments, then it should be as simple
as:

load file1.pdb
load file2.pdb

align file1//B//CA, file2//B//CA

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:delsci@delsci.info


> -----Original Message-----
> From: pymol-users-bounces@lists.sourceforge.net
> [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf
> Of Carlo Zambonelli
> Sent: Thursday, March 20, 2008 11:37 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] partial alignment (super?)
>
> Hi,
> I have 2 pdb files corresponding to 2 partially overlapping proteins:
> AB' and B"C. B' and B" have similar but not identical
> structures. I want to align B' and B" so to obtain ABC. Can I
> select to align only portions of molecules? Another
> possibility is to create 2 new pdb files corresponding to B'
> and B", do the alignment and then attach back A and C, even
> though I'm not completely sure after importing A and C in the
> B'-B" alignment session, how I would correctly position A and
> C with their original orientations relative to B' and B".
> Thank you for your help!
> Carlo
>
>
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Abhianv Verma
Research Associate,
Daggett Lab,
Benjamin Hall Interdisciplinary Research Building
University of Washington
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