Re: [ccp4bb] pdb format

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CCP4bb <-- 2008 <-- May 2008 <-- 14 May 2008

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Subject: refinement problem
From: parkash vimal {- dot -} parkash {- at -} HELSINKI {- dot -} FI
Date: 2008-05-14

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From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2008-05-14

Subject: Re: pdb format
From: Nicolas Soler soler {- at -} ICSN {- dot -} CNRS-GIF {- dot -} FR
Date: 2008-05-14

Hi Raja

You can use a command-line script like this one:

#!/bin/tcsh
sed -e "/ATOM/ s/'/*/g" -e "/ATOM/ s/O5T/O3T/" -e "/ATOM/ s/ADE/ DA/g"
-e "/ATOM/ s/CYT/ DC/g" -e "/ATOM/ s/GUA/ DG/g" -e "/ATOM/ s/THY/ DT/g"
<$1>refmacok_$1
cat refmacok_$1
grep ATOM
more>/dev/tty

Save the script in a new file (ex:DNArefmac.sh) and make sure it is
executable on your computer (in a terminal type chmod -x DNArefmac.sh).
I used it for rna
to convert from CNS format to refmac, and adapted it for dna.

Just put it in the same directory with your pdb then run it (ie: sh
DNArefmac.sh thing.pdb).
It will normally produce a new pdb suitable for refmac.called
refmacok_thing.pdb and also display it on the terminal.

Hope this will help.

Nicolas

Raja Dey wrote:
> Hi,
> The out pdb file from 'CNS' or from 'O' is not readable in
> 'CCP4'. I have dna and protein in my pdb file. Do you the best way to
> convert the pdb file I got from 'CNS" or from 'O' into 'CCP4' format?
> Especially CCP4 follows 1 letter code for dna whereas CNS and O follow
> 3 letter code. Looking forward to hearing from you....
> Thanks...
> Raja
>
> ------------------------------------------------------------------------
> BMR - a key player in weight issues. Know more.
>

--
Nicolas Soler
Institut de Chimie des Substances Naturelles
91190 Gif-sur-Yvette
tel 33-1-69823764
fax 33-1-69823784
http://perso.nicodam.org/

CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 14 May 2008

Previous message:
Subject: refinement problem
From: parkash vimal {- dot -} parkash {- at -} HELSINKI {- dot -} FI
Date: 2008-05-14

Next message:
Subject: looking for software
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2008-05-14