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

[Mike Marchywka]

>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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