Re: [ccp4bb] cavities in protein structures

[Boaz Shaanan]

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: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Claudia Binda <claudia.bi...@unipv.it> Sent: Tuesday, January 30, 2018 1:51 PM To: CCP4BB@JISCMAIL.AC.UK 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 Fax: +39-0382-528496 E-mail: claudia.bi...@unipv.it Web: http://www.unipv.it/biocry