Marius, Hmm...are you perhaps looking at the output before the file is closed and/or flushed? You should issue ndx.flush() or ndx.close() before attempting to use the output file. Cheres, Warren _____
From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Marius Retegan Sent: Friday, June 27, 2008 9:01 AM To: pymol-users Subject: Re: [PyMOL] writing selection to a external file 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 >> >> ------------------------------------------------------------------------- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > > > -- > 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 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
