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

Mike Marchywka marchywka at hotmail.com
Wed Sep 12 13:33:06 EDT 2007

>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 
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 

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