Re: [ccp4bb] ccp4 pdb format

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

Previous message:
Subject: ccp4 pdb format
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-20

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Subject: coot and stereochemistry
From: Laurent Maveyraud laurent {- dot -} maveyraud {- at -} IPBS {- dot -} FR
Date: 2007-03-20

Subject: Re: ccp4 pdb format
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-20

SHELXD writes the heavy atom coordinates both as a SHELX format .res file
(useful for spotting special positions as well as inputting into SHELXE)
and a .pdb file. Unfortunately you need to edit the name of the space
group into the first line of this PDB file (leave one space after the last
cell dimension, and a space between each part of the space group symbol)
so that most CCP4 programs can read it. This is because SHELXD only
knowns the symmetry operators, not the name of the space group. I hope
to find a fix for this in the next version of SHELXD but using the
symmetry operators instead of the space group name has the advantage that
non-standard space group settings can be handled completely unambiguously
(see the recent CCP4bb discussion on this topic). Note that Coot can read
the .res file directly and so if you just want to display the heavy atoms
in Coot you don't need to edit the .pdb file.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582

On Tue, 20 Mar 2007, yang li wrote:

> Hi:
> Now I need to input a heavy atom pdb file in the ccp4 interface, does
> ccp4 has a special format for all the programs in the package? I used
> heavy atom file from shelxd but it seemed not right. where can I get a
> model of such pdb file? Thanks!
>

CCP4bb navigation

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

Previous message:
Subject: ccp4 pdb format
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-20

Next message:
Subject: coot and stereochemistry
From: Laurent Maveyraud laurent {- dot -} maveyraud {- at -} IPBS {- dot -} FR
Date: 2007-03-20