Re: [ccp4bb] search-and-replace

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CCP4bb <-- 2007 <-- April 2007 <-- 29 April 2007

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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

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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

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

shekeb.khan@UTORONTO.CA wrote:

> 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
>
You can assign a sequence to a pdb file in Xfit for example, but it will
replace the sidechain only with the top rotamer, so you will have to
walk through your chain and actually fit it to your density.

If I remeber it correctly also arp/wARP has such a feature to assign a
sequence to a pdb file.

You can also run Molrep and assign a sequence and then stop molrep and
take the assigned.pdb file.

Not sure if Coot 0.3.1 sports this feature now, it was always planned,
but not sure if ever implemented.

Jürgen

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002

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CCP4bb <-- 2007 <-- April 2007 <-- 29 April 2007

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