Re: [ccp4bb] refmac and coot library file creation difficulty

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

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Subject: Re: refmac and coot library file creation difficulty
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-06-04

James Murphy wrote:
>
>
> I need to model in tetrachloroaurate molecules into a structure, from
> our heavy atom soak of Potassium tetrachloroaurate.
>
>
>
> I created a pdb file by using chemdraw and exporting as an *.sdf and
> opening in pymol and saving as a *.pdb (attached)

The method you used to generate the PDB/cif file has several pathologies.

1) Lowercase characters (lowercase is used in the PDB file and
upper case in the cif file)
2) The element identifiers in the PDB file are offset to the right
3) The atom names in the PDB file are offset to the right

>
> Also, coot does not draw bonds between the atoms.

Rev 2042.

Paul.

CCP4bb navigation

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

Previous message:
Subject: phaser
From: Aaron Alt aaron {- at -} IBV {- dot -} CSIC {- dot -} ES
Date: 2009-06-04

Next message:
Subject: BEST software package
From: Joe Brunzelle joeb {- at -} LS-CAT {- dot -} ORG
Date: 2009-06-04