Re: [PyMOL] Display metal coordination

[Thomas H. <tho...@sc...>]

Hi Markus and Joel,

Would something like this address your needs?

# show metal contacts
distance metalcoordination, metals, (donors acceptors), 3.5, label=0
# show metals as semi-transparent spheres
show spheres, metals
set sphere_transparency, .5
# show the metal neighbors as lines
show lines, byres (all within 3.5 of metals)

The "metals" selector was added in PyMOL 1.6.1.

Cheers,
  Thomas

> On Aug 24, 2018, at 1:29 AM, Joel Tyndall <joe...@ot...> wrote:
> 
> Hi Markus,
> 
> I am not aware of this function in pymol but would be interested in one being developed.
> 
> J
> 
> -----Original Message-----
> From: Markus Heller <mh...@cd...> 
> Sent: Friday, 24 August 2018 6:28 AM
> To: pym...@li...
> Subject: [PyMOL] Display metal coordination
> 
> Hi all,
> 
> Is there a way to display the coordination of a metal, e.g. Zn2+ or Mg2+, that doesn't require manual selection of atoms and showing of bonds?
> 
> I wasn't able to find anything online ...
> 
> Thanks
> Markus

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.