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Extracting ligands

Oct 29, 2012 at 3:00 PM

Greets, guys.

I'm looking at ways to extract the ligands from a PDB structure. Just being able to individuate the HET entries would do, as I could then filter for HOH and the such. Is there a way to do this with the parsers?


Thanks!

Oct 29, 2012 at 3:09 PM
Edited Oct 29, 2012 at 3:10 PM

Just to clarify, in Biopython this is rather straightforward by picking up those residues that have "H_" as the first two characters in the first element of the "id" tuple, e.g:

(' ', 352, ' ')
(' ', 353, ' ')
('H_MRD', 354, ' ')
('H_MRD', 355, ' ')
('H_MRD', 356, ' ')
('H_MPD', 357, ' ')
('H_ CA', 358, ' ')
('H_ CA', 359, ' ')
('H_ CA', 360, ' ')
('H_ CA', 361, ' ')
('H_ CA', 362, ' ')
('H_ CA', 363, ' ')
('H_ NA', 364, ' ')
('H_ NA', 365, ' ')
('W', 366, ' ')
('W', 367, ' ')

Thanks!

Coordinator
Oct 29, 2012 at 3:25 PM

Unfortunately this is currently not supported. I think one way to do it would be to extend the base parser with a new method that specifically reads and returns the HET entries.

Oct 29, 2012 at 3:34 PM

Right, I see.

Well, no bother, I'll work around it for now and maybe think about the implementation in the future.

Thanks!