Joosten
Date: Fri, 15 Jan 2010 14:51:45 +0100
From: daniel.schlie...@tuxomania.net
Subject: Re: [ccp4bb] DSSP server
To: CCP4BB@JISCMAIL.AC.UK
Hi Jane,
the Whatif server lists the secondary structure according to DSSP.
http://swift.cmbi.ru.nl
Hi Jane,
the Whatif server lists the secondary structure according to DSSP.
http://swift.cmbi.ru.nl/servers/html/index.html
- Protein analysis - Secondary Structure, symmetry and accessibility
Best regards, Daniel
--
Daniel Schlieper email: daniel.schlie...@tuxomania.net
Hello all,
I am sorry for this off-topic question. I see it has been discussed many
times, but somehow I got stuck in the very beginning.
I want to assign ss to my pdb file in DSSP, but I could not find a
server to run it. Does anybody know a webserver where I could run this
kind of tasks?
Hello Jane,
if I remember correctly, rasmol uses the dssp algorithm for the secondary
structure assignment. You can also use pymol or molscript (molauto) for
the same task. In any case you should always check the boundaries of the
secondary structure elements manually because no program is
Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jane Bailey
Sent: Thursday, January 14, 2010 9:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DSSP server
Hello all,
I am sorry for this off-topic question. I see it has been discussed
many
times
Hello Jane,
CMBI (http://swift.cmbi.kun.nl/gv/dssp/) offers the source code after
signing a licence agreement. I compiled it on my Mac using one of the
compile-scripts that came with the tar file. You have to install the Mac
developer package Xcode (free from developer.apple.com) for getting
Hi,
you can use the nice tool dssp2pdb by James Stroud
(http://structure.usc.edu/dssp2pdb) to assign the ss of the DSSP output
to your pdb file. See instructions there.
HTH
Guenter
I am sorry for this off-topic question. I see it has been discussed
many times, but somehow I got stuck in
On Thu, Jan 14, 2010 at 7:02 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
you could use ksDSSP, which is an OpenSource implementation of DSSP.
Requires some compiling though and I am not sure if OSX is supported.
You also need to compile the PDB record I/O libraries.
It runs
