Great, thanks 2011/8/22 Troels Emtekær Linnet <tlin...@gmail.com>
> Check this page: > http://pymol.sourceforge.net/newman/user/S0220commands.html > On the middle of the page. > > you would probably need: > select id 2338 or > select index 2338 (Probably this) > > The id, is the id number which is provided external in the pdb file. > Normally the column after "ATOM". > Beside the id number, pymol assign an internal index. > This is handsome, if your xyz file, pdb file does not have an id. > > > > > Troels Emtekær Linnet > Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> > 04107 Leipzig, Tyskland > Mobil: +49 1577-8944752 > > > > 2011/8/22 Yotam Avital <yota...@gmail.com> > >> The xyz <http://en.wikipedia.org/wiki/XYZ_file_format> file format >> opens easily with pymol (pymol fileName.xyz). I can find the id that >> pymol gives to the ``atom'' via the GUI but I don't know what to do with it. >> I tried select 2338 (a valid number) but I get >> >> Selector-Error: Invalid selection name "2338" >> >> 2011/8/22 Troels Emtekær Linnet <tlin...@gmail.com> >> >>> Is this a .pdb file which can be opened with pymol? >>> >>> Can you provide a file that pymol accepts? >>> Can you in some way find the id number? >>> Check out these commands in pymol: >>> >>> >>> print cmd.get_names() >>> print cmd.get_pdbstr("chain A") >>> print cmd.get_pdbstr("chain A").splitlines() >>> print cmd.get_pdbstr("chain A").splitlines()[3] >>> print cmd.identify("chain A and name N")[0] >>> print cmd.identify("chain A and name C")[-1] >>> >>> Troels Emtekær Linnet >>> Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> >>> 04107 Leipzig, Tyskland >>> Mobil: +49 1577-8944752 >>> >>> >>> >>> 2011/8/22 Yotam Avital <yota...@gmail.com> >>> >>>> Hi. >>>> >>>> I have a xyz file in the following form: >>>> >>>> C 0 0 0 >>>> O 0 0 1 >>>> O 0 0 2 >>>> C 0 0 6 >>>> O 0 0 5 >>>> O 0 0 4 >>>> . >>>> . >>>> . >>>> >>>> How can I select an atom from the list? How can I measure an atom from >>>> that list? >>>> -- >>>> My other email account has a "professional" signature. >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> uberSVN's rich system and user administration capabilities and model >>>> configuration take the hassle out of deploying and managing Subversion >>>> and >>>> the tools developers use with it. Learn more about uberSVN and get a >>>> free >>>> download at: http://p.sf.net/sfu/wandisco-dev2dev >>>> >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>>> >>> >>> >> >> >> -- >> My other email account has a "professional" signature. >> >> > -- My other email account has a "professional" signature.
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