VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 29 2020 - 21:50:01 CDT

Hi,
  You can set the VMD color scale color scheme and value range
for whatever the most appropriate range is for your potential field.
By default, VMD uses an RWB color scale, but you can change it to BWR
if you prefer. In the Graphical Representations window, you can
use the "trajectory" tab to control the "color scale data range"
so that you get strong coloration by your min/max potenial values.
With potential maps, rather than taking the maxima/minima like VMD
would normally do, you will get stronger coloration by selecting
max/min values that are perhaps 70% of the two min/max values in
your data. I don't know what ORCA exports, but a lot of programs
that write out potential maps do very little to prevent the grids
from containing critical points that have huge magnitude values,
and this can cause dull coloration if you allow VMD (or any program)
to use the absolute max/min values as the color scale endpoints.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 29, 2020 at 12:07:20PM +0200, Francesco Pietra wrote:
> Hallo Sebastian
> It is not a single molecule. There are several, so that the more the
> surface extends away from the nuclei, the lesser can the different
> molecules be distinguished. And by using licorice, and either transparent
> or translucent, I can't see the skeletons. Still my fault, no doubt.
> What I could never obtain with my system is blue for high potential and
> red for low potential, unlike with the water molecule. Is ORCA responsible
> for that arrangement of colors? (the water molecule was from the web, with
> cube files generated from GAUSSIAN software). I am saying that because
> with JMOL I get acceptable plots for my system (and the underlying
> skeletons are clearly distinguishable) while the colors are blue for low
> potential and red for high potential (the negatively charged oxygens of
> phosphate are intense red)
> Best
> francesco
> On Wed, May 27, 2020 at 4:36 PM Sebastian Reiter
> <[1]Sebastian.Reiter_at_campus.lmu.de> wrote:
>
> Hello Francesco,
>
> it still looks a bit strange in my opinion. An additional point you
> could try is using a smaller isovalue to get a surface further away from
> the nuclei. This will likely give you both a smoother surface and a more
> expressive colormap for the ESP. A nice demonstration of this can be
> found on Felix Plasser's blog:
> [2]https://chemical-quantum-images.blogspot.com/2019/09/esp-with-different-isovalues.html
>
> Best
> Sebastian
>
> Am 27.05.20 um 16:23 schrieb Francesco Pietra:
> > Hallo Sebastian
> > I have resumed my trials with plotting the electrostatic potential
> onto the
> > eldens. Following your recipe, with Gaussian standard files for water
> I
> > have now obtained a fully satisfactory image with values far from
> > -0.15/+0.15 (attached screenshot, I forgot to add the skeleton)
> >
> > This is good starting point to understand whether the eldens/pot files
> > (which do not obey the Gaussian standard, in fact can't be opened with
> > MOLDEN) for my system are of low quality or my dealing with them was
> > inadequate.
> >
> > thanks a lot
> >
> > ---------- Forwarded message ---------
> > From: Francesco Pietra <[3]chiendarret_at_gmail.com>
> > Date: Tue, May 26, 2020 at 9:54 AM
> > Subject: Re: Fwd: vmd-l: Fwd: Electrostatic potential maps
> > To: Sebastian Reiter <[4]Sebastian.Reiter_at_campus.lmu.de>, VMD Mailing
> List <
> > [5]vmd-l_at_ks.uiuc.edu>
> >
> >
> > Hallo Sebastian
> > With the last corrections (next to Volume mep.cube; next to Range
> > eldens.cube), and having also loaded [6]the.xyz file and using
> Transparency
> > and Tachyon rendering, it works. However, by playing around -015/0.15
> I
> > could not do better than in the attached screenshot.
> >
> > I have used extensively VMD through the years, except for rendering
> images,
> > so that I assume that I am not exploiting the VMD capabilities to this
> > concern. Such a poor graphics, and colors far from representing the
> > electrostatic potential, can't be due to a small grid.
> >
> > Thanks a lot for all your guidance
> >
> > francesco
> >
> >
> > On Mon, May 25, 2020 at 6:45 PM Sebastian Reiter <
> > [7]Sebastian.Reiter_at_campus.lmu.de> wrote:
> >
> >> Hi Francesco,
> >>
> >> no worries, that's what the mailing list is for ;)
> >>
> >> The way you describe it, you're mapping the density onto the ESP, but
> >> you actually need it the other way round. That means, next to
> "Volume"
> >> you need to choose "mep.cube" and next to "Range" choose
> "eldens.cube".
> >> Then, the color map should look right.
> >>
> >> Unfortunately, I have no experience with Chimera, but VMD has given
> me
> >> excellent results in the past. You can also make the Isosurface
> >> transparent (choose Material -> Transparent) and add another
> >> representation for the molecular skeleton structure (Licorice is
> usually
> >> a good choice). The transparency effect will look much nicer once you
> >> render the scene with VMD's render engine Tachyon.
> >>
> >> Best
> >> Sebastian
> >>
> >> Am 25.05.20 um 18:04 schrieb Francesco Pietra:
> >>> Hallo Sebastian
> >>> By playing a lot around -0.15 and +0.15 in the "Color Scale Data
> Range",
> >> I
> >>> could not do better than in the attached screenshot.
> >>> In the "Draw style" window, for Coloring Method I choose "Volume"
> and
> >> right
> >>> to Volume, I choose eldens.cube.
> >>> Right to "Range" I choose mep.cube.
> >>>
> >>> I am not mailing to VMD because I have another question. Did you try
> >> these
> >>> affairs with CHIMERA? For the same grid as here it has a perfect
> graphics
> >>> and with transparency it allows visualizing the molecular skeletons.
> It
> >>> also allows a good 3D. It only requires the mep.cube and I succeeded
> >>> immediately in plotting the electrostatic potential on a surface
> with
> >>> correct colors ( neat blue for high potential, neat red for low
> >> potential).
> >>> I did not take notice of the commands that I used and thereafter I
> am no
> >>> more able to plot on the surface. Always the plot goes to the volume
> and
> >>> therefore it does not accept colors.
> >>>
> >>> I can well imagine that your patience is exhausted. I can only thank
> you
> >>> francesco
> >>>
> >>> On Mon, May 25, 2020 at 4:56 PM Sebastian Reiter <
> >>> [8]Sebastian.Reiter_at_campus.lmu.de> wrote:
> >>>
> >>>> Hi Francesco,
> >>>>
> >>>> glad it works now. You're almost there, just make sure the density
> cube
> >>>> is selected in the dropdown menu for the Isosurface and try
> something
> >>>> like -0.15 and 0.15 for the minimum and maximum of the color range.
> If
> >>>> you want to improve the quality of the surface, you need to specify
> a
> >>>> finer grid in the orca_plot and mep.py steps.
> >>>>
> >>>> Best
> >>>> Sebastian
> >>>>
> >>>> Am 25.05.20 um 16:31 schrieb Francesco Pietra:
> >>>>> Hi Sebastian
> >>>>>
> >>>>> Thanks for the detailed instructions.
> >>>>>
> >>>>> I already had most files, except the full SCF electron density in
> cube
> >>>>> format that have now generated according to your recipe.
> >>>>>
> >>>>> As you can see from the attached screenshots, SELECTION succeeded,
> >> except
> >>>>> for the horrible graphics.
> >>>>>
> >>>>> With TRAJECTORY, I was unable to tune the color, in particular
> >> obtaining
> >>>> a
> >>>>> single color, not the desired blue-white-red according to the
> charge
> >>>>> distribution. I also tried color by charge but it did not work.
> >>>>>
> >>>>> I could not realize were I am wrong.
> >>>>>
> >> sd
>
> References
>
> Visible links
> 1. mailto:Sebastian.Reiter_at_campus.lmu.de
> 2. https://chemical-quantum-images.blogspot.com/2019/09/esp-with-different-isovalues.html
> 3. mailto:chiendarret_at_gmail.com
> 4. mailto:Sebastian.Reiter_at_campus.lmu.de
> 5. mailto:vmd-l_at_ks.uiuc.edu
> 6. http://the.xyz/
> 7. mailto:Sebastian.Reiter_at_campus.lmu.de
> 8. mailto:Sebastian.Reiter_at_campus.lmu.de 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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