John Pak wrote:
Hi, sorry if this was posted earlier. How can I calculate a
Ramachandran plot, but output the information to a text file list?
i.e. something like Ala51, phi=X, psi=Y.
I can't seem to find this information in the ccp4 SFCheck/Procheck log
file.
I thought PROCHECK listed
However, procheck ramachandran is deprecated these days as it is based
on older data than say molprobity. Obviously that won't matter just for
a list of phi/psi angles, but might affect selections e.g. what it
thinks are in a helix (cf Eleanor's message)
m
On Wed, 2009-01-14 at 14:39 -0500,
Hi,
How about STAN server at Uppsala?
http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
I suppose you can find what you are looking for at MOLEMAN2
main-chain analysis in the output webpage.
Takanori
From: John Pak john@utoronto.ca
Subject: [ccp4bb] Ramachandran plot, in a text list
Thanks for the replies everyone. I ended up using CNS_SOLVE 1.1 to
generate the Ramachandran list.
I don't seem to have access to the .rin file you mentioned. The only
output I get from Procheck are the log file and the various postscript
files. No big deal, perhaps it's because I'm
Hi, sorry if this was posted earlier. How can I calculate a
Ramachandran plot, but output the information to a text file list?
i.e. something like Ala51, phi=X, psi=Y.
I can't seem to find this information in the ccp4 SFCheck/Procheck log file.
Hi,
you can do it PHENIX (http://www.phenix-online.org/):
phenix.ramalize model.pdp
and it will give you this list.
Pavel.
PS You need to have the latest version of PHENIX for this.
On 1/14/2009 10:05 AM, John Pak wrote:
Hi, sorry if this was posted earlier. How can I calculate a
Hi John,
Another way to get at this data is to run your structure through
MolProbity (http://molprobity.biochem.duke.edu/). After this on the
mainpage there in the downloads section...if you go to *all
downloads*... there is a raw_data section that contains the
ramachandran stats
John Pak wrote:
Hi, sorry if this was posted earlier. How can I calculate a
Ramachandran plot, but output the information to a text file list?
i.e. something like Ala51, phi=X, psi=Y.
I can't seem to find this information in the ccp4 SFCheck/Procheck log
file.
And lets not forget
