Re: [ccp4bb] Calculating volume of Ligands

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CCP4bb <-- 2008 <-- January 2008 <-- 16 January 2008

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Subject: Re: Calculating volume of Ligands
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-01-16

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Subject: Re: Calculating volume of Ligands
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-16

Subject: Re: Calculating volume of Ligands
From: harry powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-01-16

Hi

A simple trick that small molecule crystallographers have been using
for decades is based on the average volume of non-hydrogen atoms
being about 18 Å^3 (this is close to being more-or-less correct for
C, N and O, and the presence of one or two S or P atoms usually makes
little difference) - they simply multiply the number of non-H atoms
in the ligand by 18 and - hey presto!

If you've only got a few atoms in your ligand, this is dead easy and
you don't need a program to do it. If you're in a hurry, use 20Å^3
instead for a slight overestimate...

On 15 Jan 2008, at 21:39, Rajan Pillai wrote:

> Hi All,
>
> Can anyone tell me any program that calculates voume of a ligand?
> Moreover, is there also any program that can calculate the volume
> of a ligand from its coordinates?
>
> Thanks,
>
> Rajan.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

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CCP4bb <-- 2008 <-- January 2008 <-- 16 January 2008

Previous message:
Subject: Re: Calculating volume of Ligands
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-01-16

Next message:
Subject: Re: Calculating volume of Ligands
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-16