[BiO BB] How to download Protein complexes from PDB ?

[Narcis Fernandez-Fuentes]

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 
> cytochrome
> 
> $ more asdf
> 
> 1: 2HL7
> Crystal Structure Of The Periplasmic Domain Of Ccmh From Pseudomonas 
> Aeruginosa
> [mmdbId:47389]
> 2: 2Z3U
> Crystal Structure Of Chromopyrrolic Acid Bound Cytochrome P450 Stap 
> (Cyp245a1)
> [mmdbId:47341]
> 3: 2Z3T
> Crystal Structure Of Substrate Free Cytochrome P450 Stap (Cyp245a1)
> [mmdbId:47340]
> 4: 2V0M
> Crystal Structure Of Human P450 3a4 In Complex With Ketoconazole
> [mmdbId:47321]
> 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:
> 
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=structure
> 
> 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.
> Thanks.
> 
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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)