Re: [ccp4bb] Calculating volume of Ligands
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
Re: [ccp4bb] Calculating volume of Ligands
It isnt a bad approximation for any organic compound to take the number of atoms including hydrogens, and multiply it by 10A^^3 Eleanor Dodson 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.
Re: [ccp4bb] Calculating volume of Ligands
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: [EMAIL PROTECTED] _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] 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.
[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.
Re: [ccp4bb] Calculating volume of Ligands
ccp4 includes a program called 'volume' that does this. see 'man volume' for a description, or $CCP4/html/volume.html Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 15 Jan 2008, 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.
