This sounds like a job for SPASM. We used it to find instances of left-handed
helices in the PDB. See:
- SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419
- Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737
The database for SPASM hasn't been updated for a few years, but it may give
you some leads.
It's probably easiest to use Mark Harris' SPASM server in Uppsala:
http://eds.bmc.uu.se/eds/spana.php?spasm=true
Brief help: http://eds.bmc.uu.se/eds/spasm_help.html
SPASM manual: http://xray.bmc.uu.se/usf/spasm_man.html
Good luck!
--Gerard
On Thu, 1 Nov 2012, eugene.krissi...@stfc.ac.uk wrote:
CCP4's gesamt should help you here. It can search a collection of PDB/mmCIF
files for a structural match, any mainchain fragment with C-alphas would do.
For searching through an archive, you need to use it off-line, from a terminal
window. Run $CCP4/bin/gesamt without parameters, it will print usage
instructions, you need 2nd or 3rd command line template depending on how you'd
like to specify your query fragment.
Beware that SSM/Superpose is not the best choice here and may not work at all.
Gesamt should be reasonably fast on short fragments, I'd expect that execution
time will be that required for opening/reading all files in the PDB :)
Hope this helps,
Eugene
On 31 Oct 2012, at 15:31, rui wrote:
Does anyone know a good way to search for a fragment matches(~16 residue long
helix or loop) from pdb?I have a fragment of pdb and want to pull out all the
similar structures from the pdb, any easy way to do that? Thanks a lot.
On Tue, Oct 30, 2012 at 9:34 AM, David Briggs
<drdavidcbri...@gmail.com<mailto:drdavidcbri...@gmail.com>> wrote:
Hello Adrian,
I use Research Gate and there are a few occasions where I have found
it useful, particularly the "questions" feature.
HTH,
Dave
============================
David C. Briggs PhD
http://about.me/david_briggs
On 30 October 2012 16:13, Adrian Goldman
<adrian.gold...@helsinki.fi<mailto:adrian.gold...@helsinki.fi>> wrote:
Hi,
At the risk of starting another series of rants, and somewhat off-topic, is
anyone actively using ResearchGate? It is bombarding me with email
messages, but I am uncertain as to whether people are really using it or
whether it is just scientific spam.
Adrian Goldman
Adrian Goldman
Institute of Biotechnology, University of Helsinki, Finland
--
Scanned by iCritical.
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
******************************************************************
