Re: [PyMOL] Spheres for metal ions

[Robert C. <rob...@qu...>]

Hi Gary,

On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter
<gar...@um...> wrote:

> I am displaying pdb files of metalloenzymes, and like to show the metal ions
> as spheres.
> I select the metal and use show>spheres
> Fine
> Somehow recently I must have done something to reset the vdw radius of
> manganese (MN in the pdb), as Mn atoms now display as small spheres (a
> little larger than solvent as nb_spheres).
> They were fine originally (!) and other metal atoms display at correct sizes
> (much bigger than my Mn).
> What could I have done?
> 
> A global edit of sphere_scale etc. simply changes all.
> I reset the setting>edit_all using the dialog as a check too.
> I can use:
> Alter name MN, vdw=vdw*2
> Rebuild
> 
> Or whatever, but I have to do it for each pdb file I read in now (if it has
> a Mn atom).
> Could I have messed with the vdw value in some way?
> 
> Is there a way to actually check the values being used for vdw radii?

You can get the vdw radii for any items (say you have a selection called
"metals") with:

  iterate metals, print chain, resn,resi,vdw

which will print the chain ID, residue name, residue number and van der Waals
radius for each.  Of course, this only applies to the vdw radius that is
assigned after you read in the PDB file.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc