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Re: [ccp4bb] search-and-replace
 

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CCP4bb <-- 2007 <-- April 2007 <-- 29 April 2007
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Subject: Re: search-and-replace
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-04-29 		Next message:
Subject: Superimposing maps from different crystal forms - solved
From: Andrew Robinson arobinso {- at -} CBMS {- dot -} MQ {- dot -} EDU {- dot -} AU
Date: 2007-04-29


Subject: Re: search-and-replace
From: Shekeb Khan shekeb {- dot -} khan {- at -} UTORONTO {- dot -} CA
Date: 2007-04-29
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)" :

>
> 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 shekeb.khan@UTORONTO.CA
> 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: shekeb.khan@utoronto.ca
Tel: +1-416-581-7548
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