Hi Anasuya,
> I have around 19,200 unique PDB files. Each of them have one or more
> ligands in it. For each ligand, I have to extract a zone which
> contains complete residues within 4.5Angstroms of the ligand [ i.e.
> ZONE1] and then extract another zone, which has complete residues
> within 4.5
hi all,
I am writing this email with regards to the following problem.
Statement of the problem:
I have around 19,200 unique PDB files. Each of them have one or more ligands in
it.
For each ligand, I have to extract a zone which contains complete residues
within 4.5Angstroms of the ligand [ i.e.
>From a purely structural perspective you can look at the interface
residues script on the PyMOLWiki:
http://pymolwiki.org/index.php/InterfaceResidues
The interface could be detected by
run /path/to/interfaceResidues.py
fetch 1bm2
interfaceResidues 1bm2, c. A, c. L
But, you ma
Dear Kousik,
Sue Jones PROTORP server should do the trick:
http://bioinformatics.sussex.ac.uk/protorp
Cheers,
Thomas
On Wed, Dec 9, 2009 at 14:57, Kousik Kundu
wrote:
>
> Dear Sir,
> I, Kousik Kundu, am a Ph.D student at university of Freiburg,
> Germany. I am using Pymol for my rece
Dear Sir,
I, Kousik Kundu, am a Ph.D student at university of Freiburg,
Germany. I am using Pymol for my recent work. I need to to the
amino acids involve in an interaction. For example 1BM2 (PDB id)
is a complex of a SH2 domain and a small peptide. Here i want to
know which amino acids (
