RE: [PyMOL] H-bond display

[Gareth S. <ga...@eb...>]

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
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.net email is sponsored by: VM Ware
> > With VMware you can run multiple operating systems on a single
> machine.
> > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
> the
> > same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute