Hi,
It seems that I run into a little problem. When I try to write a large
selection I get only a partial list of ID. If for example I print ID after
the iterate command, all the list is printed into pymol window. Do you have
any idea why?
I run Pymol 1.1pre5 under Fedora 8.
On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi,
>
> This should've gone to the list... (isn't there an option "send
> replies to list rather than to poster" to the mailing list?)
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
> > Hi Marius,
> >
> > You want iterate.
> > You do have to make sure though that the numbering of your atoms in
> > the structure file is correct. Than you can do:
> >
> > ndx=open("index.ndx","w")
> > ndx.write("[ MyIndex ]\n")
> > iterate selection, ndx.write("%d\n" % ID)
> > ndx.close()
> >
> > I did make the assumption that you wanted the atom id's rather than
> > the residue id's, since the latter are of no use to Gromacs.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> > <marius.s.rete...@gmail.com> wrote:
> >> Hi All,
> >> I'm using pymol to select (by residue) all the atoms around 10 angstroms
> >> from a certain atom. Now I would like to write the residue id's of my
> >> selection to an external file, so that I can integrated in the ndx file
> from
> >> Gromacs. Do you have any idea how I could do that?
> >>
> >> Thanks,
> >>
> >> Marius Retegan
> >>
> >>
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
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