On Thu, Aug 30, 2007 at 05:43:35PM +0900, Hyunchul Kim wrote:
> Hi, all
>
> I want to write a specific chain structures(protein). I tried PDBSET and
> biopython but they couldn't deal with some exceptional case.
> For example, some pdb files contain both protein structure and ligand
> structure in a given chain ID(e.g. 'A' or ' ')
>
> How can I obtain full chain structures without ligand structure by other
> methods than clicking one by one at any website.
Hello Hyunchal Kim,
It is not clear to me exactly what you want, but you can easily ask
Coot what chains are in a particular molecule and write out a
selection of those chains.
You can write a script that uses coot without starting up graphics.
The following will write out a pdb file "fragment.pdb" that is
the first chain of the input "x.pdb". Loop for various values of "x.pdb"
of course.
Paul.
(let ((imol (read-pdb "x.pdb")))
(let ((ids (chain-ids imol)))
(if (> (length ids) 0)
(let* ((interesting-chain-id (car ids)) ; or some such
(new-mol (new-molecule-by-atom-selection
imol interesting-chain-id)))
(write-pdb-file new-mol "fragment.pdb"))))) ; or some such
