Hi Claudia, another program that I used with success is Hollow ( https://www.ncbi.nlm.nih.gov/pubmed/19014592). It is really easy to use. You can get is here http://hollow.sourceforge.net/ It finds pockets in a defined area, fills them with water molecules and generates a pdb with those waters. You can then import it into pymol and represent it however you think is fitting.
Cheers, Johannes 2018-01-30 14:20 GMT+01:00 Vipul Panchal <[email protected]>: > Hi Claudia, > For the identification of cavities and residues linning them, metapocket > is one of the preferred choice as it uses prediction from various program. > Output of the server is pdb file. > > I found caver program represent cavities in a best manner. There is caver > plugin available for pymol. Output is tunnel like representation with > different colours. Interestingly, it also provides tunnel length, radius > and list of residues linning the bottle-neck of each of the cavity. As a > input for the presentation of cavities, you need to provide list of > residues lining cavities. Identified by other programs. > > All the best! > > > On 30-Jan-2018 6:28 PM, "Boaz Shaanan" <[email protected]> wrote: > > Hi Claudia, > > Another possibility is CastP: http://sts.bioe.uic.edu/castp/index.html > > They also have a Pymol plugin. I have not used this plugin since I'm > displaying the CastP o/p files in UCSF-chimera which handles them nicely. > > > Cheers, > > > Boaz > > > > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > [email protected] <[email protected]> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > > ------------------------------ > *From:* CCP4 bulletin board <[email protected]> on behalf of Claudia > Binda <[email protected]> > *Sent:* Tuesday, January 30, 2018 1:51 PM > *To:* [email protected] > *Subject:* [ccp4bb] cavities in protein structures > > Hi everyone, > > I need suggestions to calculate and represent cavities of protein > structures. For years I have been using Voidoo that produces maps in ezd > format which could be converted in map format (ccp4) using the online > server http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl. However, > this does not work anymore. Is there another way to do it? What is the best > tool to calculate cavities and draw them by Pymol or ccp4mg? > > Thank you > Claudia > > > > > > > > -- > Claudia Binda > University of Pavia > Dept. Biology and Biotechnology > via Ferrata 1, 27100 Pavia - Italy > Phone: +39-0382-985535 <+39%200382%20985535> > Fax: +39-0382-528496 <+39%200382%20528496> > E-mail: [email protected] > Web: http://www.unipv.it/biocr <http://www.unipv.it/biocry> > >
