VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Aug 04 2018 - 09:59:04 CDT

Vladimir,
  Can you send me the molden file and a VMD saved state that show
the clipped orbital? There is a routine in VMD that computes the
required size of the bounding box for the orbital by evaluating
the orbital amplitude along the x/y/z axes. If you can give me
the case that breaks for you I can either adjust the scheme VMD
uses to compute the bounding box and/or add an option to expand
the bounding box by some marginal factor, or something similar.

Best,
  John Stone

On Sat, Aug 04, 2018 at 03:10:18PM +0300, Vladimir Stegailov wrote:
> Hello,
> please let me know of if it is possible to change (to increase)
> the bounding box that VMD uses when it displays molden orbitals.
> This bounding box cuts the isosurfaces.Â
> It causes problems for visualizing diffusive orbitals.
> As far as I understand (and have checked), the commands like
> pbc set {10.0 10.0 10.0} -all
> do not change this particular bounding box size.
> The bounding box size is not defined in the molden file itself.Â
> Presumably, VMD uses some guessing mechanism to set it?
> Vladimir 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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