[BiO BB] How to download Protein complexes from PDB ?
skhadar at gmail.com
Thu Sep 13 07:38:37 EDT 2007
Thanks for your reply.
> 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
> 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
> 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
You can download whole PDB from RCSB. Goto
Click on Download, you can go with FTP download to download the full pdb.
seperate dirs are avaialable. you can write a wget based script to get the
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