Re: [PyMOL] partial alignment (super?)

[Abhinav V. <abh...@gm...>]

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 <de...@de...>
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:de...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf
> > Of Carlo Zambonelli
> > Sent: Thursday, March 20, 2008 11:37 AM
> > To: pym...@li...
> > 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
Box 355013
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