[BiO BB] How to download Protein complexes from PDB ?
narcis at fiserlab.org
Wed Sep 12 13:44:18 EDT 2007
just use pdb advanced search engine
Mike Marchywka wrote:
>> I need to download a set of 200 complexes from PDB (they can include
>> dimers, trimers and tetramers). But they should only contain
> I'm not entirely sure what you mean but I do know I've had to guess a lot
> with the ncbi structure database. To test my molecule viewer, I had to
> write several
> new scripts like this:
> 142 pdbget -out xxx -structure "gaba complex"
> 143 cat xxx
> 144 pdbget -get 29354 1sff.pdb
> I've got another script that the above calls:
> $ eutilsnew -v -out asdf -structure -report docsum -retmode text
> $ more asdf
> 1: 2HL7
> Crystal Structure Of The Periplasmic Domain Of Ccmh From Pseudomonas
> 2: 2Z3U
> Crystal Structure Of Chromopyrrolic Acid Bound Cytochrome P450 Stap
> 3: 2Z3T
> Crystal Structure Of Substrate Free Cytochrome P450 Stap (Cyp245a1)
> 4: 2V0M
> Crystal Structure Of Human P450 3a4 In Complex With Ketoconazole
> 5: 2NZA
> I can't find a spec that say, "return all the matching pdb's", I just
> get a list of id's
> and have to go get the ones I want. Still easy to automate however.
> Search criteria are here:
> I generally take the "download everything close and sort it out locally
> approach" using custom scripts for one-off searches.
> If anyone knows the codes to download all the pdb's at once can you
> please post.
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Narcis Fernandez-Fuentes, phD
Seaver Center for Bioinformatics
Albert Einstein College of Medicine
1300 Morris Park Ave, Bronx, NY 10461, USA
phone: (718)430-8564 fax: (718) 430-8565
mailto:narcis at fiserlab.org (http://www.fiserlab.org)
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