VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 29 2021 - 14:37:42 CST

Hi,
  If your density map includes potentials within the VDW radii of
the atoms in the system and you want to screen out those points, you
could try using the various VMD volumetric processing commands to
create a mask map from a synthetic density map, and then use the mask
map to zero out the potentials for grid poins within the atoms themselves.
I don't know what file format(s) you may be using so I'm not sure which
of the volumetric manipulation tools are the best match.

Alternately, another (easier) way of dealing with those is to override
the autoscaling of the color scale data range for the volume, and set
your own min/max data values used for the color scale. I don't know what
your electrostatic potential units are in your case, but you could pick
reasonable min/max potential values, and set them in the
"color scale data range" fields of the "trajectory" tab in the VMD
graphical representations window.

Let us know if you have further questions about these ideas.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 29, 2021 at 09:29:12AM -0500, Araz Jakalian wrote:
> Hello,
>
> Iâ**m successful in mapping the ESP onto the density isosurface (using
> .cube density and ESP files from psi4). The min and max ESP values are
> displayed in the trajectory tab and also on the command line.
> Â
> However, those min and max ESP values are calculated from the complete set
> of grid points, including those near the nuclei which have a very high
> positive value.
>
> Iâ**m interested in obtaining the ESP min and max values outside of the
> VDW surfaceâ*¦ from the currently set density isosurface (0.02 to 0.04)â*¦
>
> Meaning, I would like to eliminate those ESP values from inside the VDW
> radii in order to get a better understanding of the actual min and max
> values at the molecular recognition surface.
>
> The colouring of the surface by ESP seems correct but the min and max
> values are not representative of the current colours.
>
> Is there a way to obtain the min & max ESP values at the currently
> determined isosurface (either by clicking on Autoscale or printing on the
> command line)?
>
> Thank you,
> Araz Jakalian 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/