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
chapterhttps://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:
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 <tel:+39%200382%20985535>
Fax: +39-0382-528496 <tel:+39%200382%20528496>
E-mail: [email protected] <mailto:[email protected]>
Web: http://www.unipv.it/biocry
--
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.
