Re: [ccp4bb] search-and-replace

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: search-and-replace
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-04-29

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

Subject: Re: search-and-replace
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-04-29

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: search-and-replace
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-04-29

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