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,
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 <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I use Research Gate and there are a few occasions where I have found
it useful, particularly the "questions" feature.
David C. Briggs PhD
On 30 October 2012 16:13, Adrian Goldman <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> 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
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