RE: [PyMOL] H-bond display

[Warren L. D. <wa...@de...>]

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:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Gareth Stockwell [mailto:ga...@eb...]
> 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:wa...@de...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax   (650)-593-4020
> >
> > > -----Original Message-----
> > > From: pym...@li... [mailto:pymol-users-

> > > ad...@li...] 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 <ga...@eb...>
> > > European Bioinformatics Institute
> > >
> > >
> > >
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> --
> Gareth Stockwell <ga...@eb...>
> European Bioinformatics Institute