Gary Hunter 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?
Thanks
Gary
Prof. Gary J. Hunter,
Department of Physiology and Biochemistry,
University of Malta, Msida, MSD 06, Malta.
phone: +356 2340 2917
phone: +356 21316655 (secretary), Fax: +356 21310577
Gary,
You will normally have to manually adjust the ionic radius of metal ions
to correctly render them. For starters, PDB files are not always good at
distinguishing between atoms and ions; second, there is no single "ionic
radius" for metal ions, as their effective radius depends on
coordination number. (For example, zinc has different ionic radii for 4-
and 5-coordinate compounds. A simple way to adjust radii globally by
element is:
alter elem zn, vdw=0.74
rebuild
(This would set zinc in a protein structure to 0.74A, the appropriate
value for a four-coordinate metal environment.)
There are many databases out there for obtaining ionic radii. For
example, see http://abulafia.mt.ic.ac.uk/shannon/ .
Cheers,
--
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Roger S. Rowlett
Professor
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Colgate University
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