Gareth,
cmd.identify returns the input indexing, which will correspond
to the PDB file.
cmd.index returns the internal indexing, which will correspond
to cmd.get_model
help identify
help index
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: Gareth Stockwell [mailto:gar...@ebi.ac.uk]
> Sent: Friday, July 18, 2003 8:50 AM
> To: Warren L. DeLano
> Cc: 'pymol-users'
> Subject: RE: [PyMOL] H-bond display
>
> Warren,
>
> I started having a look at this, but I am getting stuck with atom
> indices. If I make two selections, (lb) and (rb), by clicking on
> atoms in an object called 'x', then I can get the indices and objects
> of those atoms by doing
>
> x1 = cmd.identify("lb",1)
> x2 = cmd.identify("rb",1)
>
> In my example, printing out x1 and x2 gives the following: [('x', 2)]
> [('x', 16)]
>
> As I clicked on these atoms, the GUI told me that they were,
> respectively:
> VAL: /x/1ATP/E/15/CA
> LYS: /x/1ATP/E/16/NZ
>
> But now, if I dump out the contents of the model.atom array, using
> this
> code:
>
> m = cmd.get_model("x")
> i = 1
> for a in m.atom:
> print str(i) + " -> " + a.chain + "/" + a.resn + "." \
> + a.resi + "/" + a.name
> i = i+1
>
> Then I see the following
> 1 -> E/VAL.15/N
> 2 -> E/VAL.15/CA
> 3 -> E/VAL.15/CB
> 4 -> E/VAL.15/CG1
> 5 -> E/VAL.15/CG2
> 6 -> E/VAL.15/C
> 7 -> E/VAL.15/O
> 8 -> E/LYS.16/N
> 9 -> E/LYS.16/CA
> 10 -> E/LYS.16/CB
> 11 -> E/LYS.16/CG
> 12 -> E/LYS.16/CD
> 13 -> E/LYS.16/CE
> 14 -> E/LYS.16/NZ
> 15 -> E/LYS.16/C
> 16 -> E/LYS.16/O
> 17 -> E/GLU.17/N
> 18 -> E/GLU.17/CA
> 19 -> E/GLU.17/C
> 20 -> E/GLU.17/O
>
> So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is
> the O, not NZ in LYS.16. I presume that ChemPy is re-ordering the
> atoms some time during the get_model call - how do I resolve this?
>
> Gareth
>
>
> On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> > Gareth,
> >
> > CGO is currently the way to go...
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > mailto:war...@delanoscientific.com
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> >
> > > -----Original Message-----
> > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > > ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell
> > > Sent: Friday, July 18, 2003 2:46 AM
> > > To: pymol-users
> > > Subject: [PyMOL] H-bond display
> > >
> > >
> > > I am using distance objects at the moment, to display h-bonding
> > > contacts. My question is ... is there any easy way to display the
> > > direction of an h-bond using distances (i.e. putting a little
> > > arrow on the dashed line)?
> > >
> > > I am prepared to bash out some functions which do this using CGOs,
> > > but of course I won't if it's already implemented!
> > >
> > > Gareth
> > >
> > >
> > > --
> > > Gareth Stockwell <gar...@ebi.ac.uk>
> > > European Bioinformatics Institute
> > >
> > >
> > >
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> --
> Gareth Stockwell <gar...@ebi.ac.uk>
> European Bioinformatics Institute
