Re: [ccp4bb] DSSP server
Dear CCP4BB-ers, The official DSSP is now also available for Intel Macs: http://swift.cmbi.ru.nl/gv/dssp/ We have limited access to Mac computers, so the software is not as thoroughly tested as the Linux and Windows versions. Feel free to send bug reports. Best wishes, Gert Vriend Robbie 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/servers/html/index.html - Protein analysis - Secondary Structure, symmetry and accessibility Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemie der Pflanzen phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40225 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
Re: [ccp4bb] DSSP server
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 Biochemie der Pflanzen phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40225 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de
[ccp4bb] DSSP server
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? I use iMAC. Many thanks! Jane
Re: [ccp4bb] DSSP server
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 perfect ;-) Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 14 Jan 2010, Jane Bailey wrote: 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? I use iMAC. Many thanks! Jane
Re: [ccp4bb] DSSP server
Jane, 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. http://www.cgl.ucsf.edu/Overview/software.html Cheers, Carsten -Original 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, 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? I use iMAC. Many thanks! Jane
Re: [ccp4bb] DSSP server
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 the C-compiler. Best regards, Dirk. Am 14.01.10 15:54, schrieb Jane Bailey: 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? I use iMAC. Many thanks! Jane -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] DSSP server
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 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? I use iMAC. Many thanks! Jane -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fr...@uni-konstanz.de Phone Office: +49-(0)7531 88 3205 Phone Lab : +49-(0)7531 88 3733 Fax: +49-(0)7531 88 2966
Re: [ccp4bb] DSSP server
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 fine on OS X, but I think I had to run 'ranlib' on the PDB library to get it to compile properly. However, I've seen at least one structure (1ywf) for which it produces incorrect results; this may not matter if you just want to make figures, but it's problematic for any other uses. I was able to download the DSSP source code from CMBI without signing anything - but it's still proprietary and only free to academics. (And I had no luck compiling it on a Mac, unfortunately.) -Nat
