I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres.
I select the metal and use show>spheres
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
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?
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