From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 20 2019 - 08:57:18 CDT

None. There VMD "color" commands that overwrite the color scale, as described
in the VMD User's Guide, and as demonstrated in the script I sent.
You just need to run the Tcl "source" command on that script to load it
(no need to replace anything in VMD itself), and then you can issue any
of the commands it contains to replace the color scale with one of the
Matlab-derived variants. You can then go further and write your own
procedures for whatever other kinds of color scales you may need.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 20, 2019 at 08:43:40AM -0500, Thomas Sommerfeld wrote:
> Hello¬ John,
> thanks for the script. Sounds simple and straightforward.
> However, there are 551 .tcl files in the vmd tree. Could you let me know
> which one I have to overwrite to replace the color-by-volume color maps?
> Thomas¬
> On Thu, Sep 19, 2019 at 9:37 AM John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> You can overwrite the default VMD color scales with anything you want
> using a trivial script.¬ I attach an example script that reproduces
> the standard matlab color scales/gradients.¬ Let me know if you have
> questions on using it or adapting it for the color scales you want to
> use.
>
> Best,
> ¬ John Stone
> ¬ [2]vmd_at_ks.uiuc.edu
>
> On Thu, Sep 19, 2019 at 09:26:14AM -0500, Thomas Sommerfeld wrote:
> >¬ ¬ OK, I admit, not so much a question, more a wish for a feature in
> the next
> >¬ ¬ version.
> >¬ ¬ If I color a volume, say a density, using the color method
> "volume", I
> >¬ ¬ have the choice between 12 colormaps. The graphics look great,
> but all 12
> >¬ ¬ colormaps are "dividing" (intended for some -a ... a range).
> >¬ ¬ What I need currently, and I should think would be useful in
> general, is
> >¬ ¬ (1) uniform colormaps, such as viridis or plasma (for ranges 0
> ... a),
> >¬ ¬ because my property may be an absolute value.
> >¬ ¬ (2) cyclic colormaps, such as hsv (for ranges 0 ... 2*pi), to map
> phases,
> >¬ ¬ molecules in magnetic fields, or just to draw psi_211 for PCHEM
> class.
> >¬ ¬ (3) colormaps like jet or rainbow, because I know many people who
> prefer
> >¬ ¬ them over (1) or (2) for some reason. Well I use them myself for
> pH, but
> >¬ ¬ not for volumes.
> >¬ ¬ Thanks for considering,
> >¬ ¬ Thomas
> >¬ ¬ ŗłĘ ŗłĘ
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/¬ ¬ ¬ ¬ ¬ ¬ Phone: 217-244-3349
> [4]http://www.ks.uiuc.edu/Research/vmd/¬ ¬ ¬
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/

-- 
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/