Re: [ccp4bb] How to number atoms in a ligand

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CCP4bb <-- 2007 <-- October 2007 <-- 08 October 2007

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Subject: Reminder, Oct 15, Deadline SLS PX Proposals
From: Heinz J Weyer heinz-josef {- dot -} weyer {- at -} PSI {- dot -} CH
Date: 2007-10-08

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Subject: Re: How to number atoms in a ligand
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-10-08

Subject: Re: How to number atoms in a ligand
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-10-08

Dear Joe,

Atom labels are, in principle, arbitrary. The molecule doesn't case
what we call its atoms. To make the PDB more useful, it is handy if
all the people working with a particular compound use the same names for
their atoms. If you find that someone has already deposited a structure
containing your compound you are expected to use the same names they did.
There are lists of compounds and naming conventions on the PDB web site.

The small molecule literature doesn't count as precedence for naming
conventions, only what is in the PDB. No one will hold you to the names
used in the small molecule structure paper.

If you are the first to work with this compound in the macromolecular
world you are free to choose whatever names you want. Please choose
something sensible as the rest of use will be stuck with your choice
forever. Consistency is king here. If a similar compound is in the
PDB, using atom names based on it would simplify comparisons.

Dale Tronrud

Zheng Zhou wrote:
> Hi, all
>
> I am a rookie in crystallography. I know this may be a little bit off
> topic. I have cocrystallized several compounds with my favorite protein.
> I found crystal structures for some of these chemicals. But the
> numbering systems are different in those original papers for the small
> molecules. Some numbering system has all the atoms from 1 to the end
> (C1-O3-O8-N9-C15), while others have numbers for each individual
> element. (C1-C12, O1-O2, N1). I was trying to search a unified theme for
> ligands in pdb. I even emailed deposit@deposit.rcsb.org
> , but so far I haven't heard anything
> back. Could anyone give me some suggestions? Any help would be greatly
> appreciated.
>
> Thanks,
>
> Sorry to bother others
>
> Joe
>

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CCP4bb <-- 2007 <-- October 2007 <-- 08 October 2007

Previous message:
Subject: Reminder, Oct 15, Deadline SLS PX Proposals
From: Heinz J Weyer heinz-josef {- dot -} weyer {- at -} PSI {- dot -} CH
Date: 2007-10-08

Next message:
Subject: Re: How to number atoms in a ligand
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-10-08