From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 24 2008 - 18:08:52 CST

Kristin,
  Just to verify that I understand what you're doing, are you rendering
isosurfaces of the same density level (in both programs) and then
comparing them visually? From your description it sounds like you've got
a different isovalue selected in the two programs, which would produce similar
but non-identical surface representations. Another possibility is that
coot did some sort of transformation on the density map that affects how
it renders in VMD but not coot? I'd check the selected isovalues first
and we can proceed with further questions later.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 23, 2008 at 10:03:12AM -0500, Kristin Wunsch wrote:
> Hello-
>
> I am trying to use VMD to display a structure with electron density in the
> CCP4 map format. When I open the map in coot there is a great deal of
> density around the active site metal. When opened in VMD this density does
> not appear around the metal but does appear in similar places as the coot
> map. I used the export-map script in coot to generate the map that I am
> opening in VMD. Is there a logical reason why this is happening? Any
> suggestions to fix this? The density around the metal is very important in
> this structure.
>
> Thank you in advance for any suggestions!
> Kristin Wunsch

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