VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 09 2021 - 15:59:52 CST

Hi,
  I just wrote another suggestion for the previous topic, which when using
evenly-spaced data values, would permit one to use the built-in color scale
GUI to generate a color scale with a specific number of colors, and then
map them to the evenly-spaced data values. For cases that are irregularly
spaced, I'm afraid one has to write a little script to generate the necessary
color scale. This however should be well within the mathematical grasp of
any scientist I should think. The examples I posted previously that reproduce
popular Matlab color scales should be plenty to work with as examples to get
started.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Nov 06, 2021 at 06:22:11PM +0000, Vermaas, Josh wrote:
> Like, what is the goal? The one last week was weird, since it looked like
> it wanted a single surface to have 4 colors. What exactly is pyMol doing
> to decide the color of the surface? I don't know. I use VMD, so how pyMol
> does stuff is a dark art. I stand by my statement from last week that VMD
> can do anything with enough scripting, but without some guidance on what
> an image represents that you want to replicate, or some info on how pyMol
> made color choices, you are just going to get generic answers.
>
>
>
> -Josh
>
>
>
> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of maxim todoru
> <mtodoru_at_gmail.com>
> Date: Saturday, November 6, 2021 at 1:45 PM
> To: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Color Transition in VMD
>
>
>
> believe me i read it before i ask my question, but the proposed solutions
> didn't fix a thing, even by using tcl scripting it's impossible to achieve
> my goal. I hope that the developers of VMD could include this
> functionnality in the future.
>
> Le samedi 6 novembre 2021, Giacomo Fiorin <[1]giacomo.fiorin_at_gmail.com> a
> écrit :
>
> This thread was only a week ago:
>
> [2]https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/33339.html
>
>
>
>
>
> On Sat, Nov 6, 2021 at 11:22 AM maxim todoru <[3]mtodoru_at_gmail.com>
> wrote:
>
> Hi,
>
> Does VMD support customizing color transitions like in Pymol software
> ?
>
>
>
> References
>
> Visible links
> 1. mailto:giacomo.fiorin_at_gmail.com
> 2. https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/33339.html__;!!HXCxUKc!koAdfKuMF0tT74aSmAwRyffwPdaUN8c-oWbbaadSPVbnlktXblSFUmhV-dfNBdY$
> 3. mailto:mtodoru_at_gmail.com 

-- 
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/