VMD-L Mailing List

From: Thomas Sommerfeld (thomas.sommerfeld_at_selu.edu)
Date: Fri Sep 20 2019 - 15:01:11 CDT

Thanks. Worked like a charm.

On Fri, Sep 20, 2019 at 8:57 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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:
> > Helloย 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?
> > Thomasย
> > 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.ย I attach an example script that reproduces
> > the standard matlab color scales/gradients.ย Let me know if you
> have
> > questions on using it or adapting it for the color scales you want
> to
> > use.
> >
> > Best,
> > ย John Stone
> > ย [2]vmd_at_ks.uiuc.edu
> >
> > On Thu, Sep 19, 2019 at 09:26:14AM -0500, Thomas Sommerfeld wrote:
> > >ย ย OK, I admit, not so much a question, more a wish for a
> feature in
> > the next
> > >ย ย version.
> > >ย ย If I color a volume, say a density, using the color method
> > "volume", I
> > >ย ย have the choice between 12 colormaps. The graphics look
> great,
> > but all 12
> > >ย ย colormaps are "dividing" (intended for some -a ... a range).
> > >ย ย What I need currently, and I should think would be useful in
> > general, is
> > >ย ย (1) uniform colormaps, such as viridis or plasma (for ranges
> 0
> > ... a),
> > >ย ย because my property may be an absolute value.
> > >ย ย (2) cyclic colormaps, such as hsv (for ranges 0 ... 2*pi),
> to map
> > phases,
> > >ย ย molecules in magnetic fields, or just to draw psi_211 for
> PCHEM
> > class.
> > >ย ย (3) colormaps like jet or rainbow, because I know many
> people who
> > prefer
> > >ย ย them over (1) or (2) for some reason. Well I use them myself
> for
> > pH, but
> > >ย ย not for volumes.
> > >ย ย Thanks for considering,
> > >ย ย Thomas
> > >ย ย เธข เธข
> >
> > --
> > 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/ย ย ย ย ย ย Phone:
> 217-244-3349
> > [4]http://www.ks.uiuc.edu/Research/vmd/ย ย ย
> >
> > 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/
>