Dear Rob
Thanks a lot.
print_hb_list.py is really what I wanted.
As I'm a beginner of python, your script is very helpful.
Thanks again,
Tomoko
2008/5/6 Robert Campbell <robert.campb...@queensu.ca>:
> Hi Tomoko,
>
> On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa <tmk.n...@gmail.com>
> 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
> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
>
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