Hi Stephen, I have a python script that does exactly that. It uses a surface calculated by MSMS and calculates the similarity using a function like that of the SC program. You'll need to align the structures first. There is an equivalent script that calculates the complementarity of two surfaces. I also have a script that reads the output of this and draws the surface in PyMOL and colours it according to the SC value at each vertex.
You can find the similarity and complementarity scripts here, along with some instructions: http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_similarity.py http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_complementarity.py The script for drawing the surface is here: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#msms_sim_draw.py Cheers, Rob On Wed, 2017-06-14 11:42 +0000, "<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: > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mrc.ac.uk%2FAbout%2Finformationandstandards%2Fdocumentmarking%2Findex.htm&data=02%7C01%7Crobert.campbell%40QUEENSU.CA%7Cd9fb9ff31c644fc370a108d4b31a83d5%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636330373846170692&sdata=2idclOFgwguyEWoaa6xLHQcGbi6l1jK3mQcyn7YzNGo%3D&reserved=0. -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
