[ccp4bb] search-and-replace

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- April 2007 <-- 28 April 2007

Previous message:
Subject: Re: buried surface area
From: Palm palm {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2007-04-28

Next message:
Subject: Postdoctoral position in protein engineering
From: Olga {- dot -} Mayans {- at -} UNIBAS {- dot -} CH Olga {- dot -} Mayans {- at -} UNIBAS {- dot -} CH
Date: 2007-04-29

Subject: search-and-replace
From: shekeb {- dot -} khan {- at -} UTORONTO {- dot -} CA shekeb {- dot -} khan {- at -} UTORONTO {- dot -} CA
Date: 2007-04-28

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 <-- 2007 <-- April 2007 <-- 28 April 2007

Previous message:
Subject: Re: buried surface area
From: Palm palm {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2007-04-28

Next message:
Subject: Postdoctoral position in protein engineering
From: Olga {- dot -} Mayans {- at -} UNIBAS {- dot -} CH Olga {- dot -} Mayans {- at -} UNIBAS {- dot -} CH
Date: 2007-04-29