[BiO BB] How to download Protein complexes from PDB ?
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
Crystal Structure Of The Periplasmic Domain Of Ccmh From Pseudomonas
Crystal Structure Of Chromopyrrolic Acid Bound Cytochrome P450 Stap
Crystal Structure Of Substrate Free Cytochrome P450 Stap (Cyp245a1)
Crystal Structure Of Human P450 3a4 In Complex With Ketoconazole
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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