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" <[log in to unmask]> 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: [log in to unmask]
Phone: 972-8-647-2220  Skype: boaz.shaanan                 
Fax:   972-8-647-2992 or 972-8-646-1710    
 
 
                



From: CCP4 bulletin board <[log in to unmask]> on behalf of Claudia Binda <[log in to unmask]>
Sent: Tuesday, January 30, 2018 1:51 PM
To: [log in to unmask]
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: [log in to unmask]
Web: http://www.unipv.it/biocr