Hi Stephen, I've had some luck calculating ligand-binding cavity volume with the 3v website (http://3vee.molmovdb.org/). You might want to give it a shot.
Best, Chris On Wed, Jun 14, 2017 at 12:42 PM, <Stephen Carr> < stephen.c...@rc-harwell.ac.uk> wrote: > Dear ccp4bb, > > I am trying to compare the shape of a ligand binding site in my protein > with that of some homologues and mutants and was wondering how others go > about this? I specifically want to compare the shapes of the surface > (similar to an sc analysis of an interface) rather than the positions of > the atoms in the residues that make up the site. I have come across > PESDserv, but this doesn't do quite what I would like. Any suggestions > would be very welcome. > > Best wishes, > > Steve > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email stephen.c...@rc-harwell.ac.uk > tel 01235 567717 > > This email and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorized recipient of the > addressee, please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > this email. > > Any views or opinions presented are solely those of the author and do not > necessarily represent those of the Research Complex at Harwell. > > There is no guarantee that this email or any attachments are free from > viruses and we cannot accept liability for any damage which you may sustain > as a result of software viruses which may be transmitted in or with the > message. > > We use an electronic filing system. Please send electronic versions of > documents, unless paper is specifically requested. > > This email may have a protective marking, for an explanation, please see: > http://www.mrc.ac.uk/About/informationandstandards/ > documentmarking/index.htm. >
