Thank you for the replies. coot 0.3.1 gave me the option of mutating
a pdb file to a semi_polyala (via mutate residue range, no map
required) but the rotamers were changed for the conserved residues.
Chainsaw worked beautifully, however, using the wildtype A.pdb and a
hand-crafted sequence alignment file in pir format as inputs.
with kind regards,
Shekeb
Quoting "Winn, MD (Martyn)" <[EMAIL PROTECTED]>:
If I understand you correctly, the CCP4 program Chainsaw would do
this.
It uses an alignment file, which you could hand-craft to select
mutate or conserve.
Keyword "MODE MIXA" to select the truncate-to-beta option.
HTH
Martyn
-----Original Message-----
From: CCP4 bulletin board on behalf of [EMAIL PROTECTED]
Sent: Sun 4/29/2007 3:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] search-and-replace
Hello everyone,
I have two pdb files for molecule A (A.pdb and A_polyala.pdb) from
which I would like to make a hybrid file A_semi.pdb. A_semi.pdb will
have some residues with full sidechains (so derived from A.pdb) and
some residues with only a C-beta atom for a sidechain (so derived from
A_polyala.pdb). The residues I would like mutated are listed in file
B.txt (in total about 250 residues to be mutated). I could do this by
hand but I figure there must be a fater way to do it. Does anyone
have any suggestions on how I might be able to do this? Is there some
unix search-and-replace command line I could use to replace all lines
of text in A.pdb containing ### (spaced appropriately) with those
lines of text in A_polyala.pdb containing the same ###, and then have
it repeat this for all ~250 residues listed in the file B.txt?
Many thanks in advance,
Shekeb
--
Shekeb Khan
Ph.D. Candidate
Department of Medical Biophysics, University of Toronto
Toronto Medical Discoveries Tower (TMDT), MaRS Centre
101 College Street, Room 5-359
Toronto, Ontario, Canada
M5G 1L7
Email: [EMAIL PROTECTED]
Tel: +1-416-581-7548
