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Hi Claudia

Two options I've used recently, liked and displayed without fuss in PyMOL are ProFunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/) and Ghecom (http://strcomp.protein.osaka-u.ac.jp/ghecom/). Ghecom gives you PDB files directly. ProFunc gives you rasmol scripts but they open fine with PyMOL. Other options are listed in this book chapter https://link.springer.com/content/pdf/10.1007/978-94-024-1069-3_10.pdf which I can email if you don't have access.

Best wishes

Daniel


On 30/01/18 11:51, Claudia Binda wrote:
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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/biocry

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Dr Daniel John Rigden                 Tel:(+44) 151 795 4467
Institute of Integrative Biology      FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool               http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.