Hi Tomoko,
On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa <[email protected]>
wrote:
> Thanks for kind advices.
>
> Whatif and PISA worked excellently, but I want to get the list within Pymol.
>
>
> By parsing the pymol modules, I found
>
> hb = cmd.find_pairs("((byres "+sss1+") and n;n)",
> "((byres "+sss1+") and n;o)",mode=1,
> cutoff=3.7,angle=55,
> state1=state,state2=state)
>
> in util.py. Is it possible to get a list of main-chain hydrogen bonds with
> this function?
Yes it is. I thought this was a useful idea, so I've just scribbled together
a script to do just that and it is attached.
You can load it the usual way ("run print_hb_list.py") and then run it
with:
print_hb <selection>
Warning, if you have waters in your selection it will mess it up, so try:
print_hb 1nzl &! resn hoh
I haven't fixed that part yet. You may wish to alter the formatting of the
output, but I copied the example in your first e-mail:
/GLY`56/N /ASN`181/O 2.86
/TYR`26/N /VAL`182/O 2.92
/ASN`54/N /THR`183/O 2.95
/ASN`52/N /TRP`185/O 2.92
In my case the PDB file had no "chain" identifier.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[email protected]> http://pldserver1.biochem.queensu.ca/~rlc
from pymol import cmd
def print_hb(selection):
hb = cmd.find_pairs("((byres "+selection+") and n;n)","((byres "+selection+") and n;o)",mode=1,cutoff=3.7,angle=55)
pair1_list = []
pair2_list = []
dist_list = []
for pairs in hb:
cmd.iterate("%s and ID %s" % (pairs[0][0],pairs[0][1]), 'print "%s/%3s`%s/%s " % (chain,resn,resi,name),')
cmd.iterate("%s and ID %s" % (pairs[1][0],pairs[1][1]), 'print "%s/%3s`%s/%s " % (chain,resn,resi,name),')
print "%.2f" % cmd.dist("%s and ID %s" % (pairs[0][0],pairs[0][1]),"%s and ID %s" % (pairs[1][0],pairs[1][1]))
cmd.extend("print_hb",print_hb)
