Re: [ccp4bb] Calculating volume of Ligands

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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

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Subject: Re: Calculating volume of Ligands
From: Isaac Westwood isaac {- dot -} westwood {- at -} PHARM {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-01-16

Dear Rajan,

In addition to the estimates already mentioned, if you have access to Chem3D
(Cambridgesoft), you can calculate the Connolly volume (excluding solvent)
for any (preferably small) molecule, either drawn by hand or by input from
its coordinates. In ChemBio3D ultra, this is found in calculations >
computer properties > ChemPropStd.

Another guestimate method is to determine the distances between various
pairs of atoms in, e.g. Coot, and to do a back-of-an-envelope calculation
for the volume based on those, but that's probably less accurate than the
estimate methods already mentioned!

Isaac

----------

Dr Isaac Westwood

Department of Pharmacology

University of Oxford

Mansfield Road

Oxford

OX1 3QT

tel: 01865 271595

email: isaac.westwood@pharm.ox.ac.uk

_____

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajan
Pillai
Sent: 15 January 2008 21:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculating volume of Ligands

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.

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

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

Next message:
Subject: Re: Perl
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-01-16