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>
