[PyMOL] partial alignment (super?)

[Carlo Zambonelli]

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

[DeLano Scientific]

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

-----Original Message-----
Of Carlo Zambonelli
Sent: Thursday, March 20, 2008 11:37 AM
Subject: [PyMOL] partial alignment (super?)
Hi,
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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[Abhinav Verma]

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.

Post by DeLano Scientific
Carlo,
If B is the chain ID for the matched seguments, then it should be as simple
load file1.pdb
load file2.pdb
align file1//B//CA, file2//B//CA
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services

-----Original Message-----
Of Carlo Zambonelli
Sent: Thursday, March 20, 2008 11:37 AM
Subject: [PyMOL] partial alignment (super?)
Hi,
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
--------------------------------------------------------------
-----------
This SF.net email is sponsored by: Microsoft Defy all
challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/pymol-users

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