VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Sat Nov 13 2021 - 15:09:15 CST

The new features of coloration scale in vmd is fabulous, and it is exactly
fit with my situation, e.g. one isosurface with four colors, but the colors
are fixed and we can't create our customized colors, even by using tcl
scripting, and many colleagues experienced in tcl not succeeded in that
purpose.

Le vendredi 12 novembre 2021, maxim todoru <mtodoru_at_gmail.com> a écrit :

> Professor Stone, we can only create no more than a customized three
> colors, but in vmd 1.9.4, the advanced colors scale like plasma viridis;
> there are more than three colors, which is perfect for my coloration
> situation, but it seems not customizable, for example I'm looking for the
> colors red, cyan, green, purple.
>
> Le mar. 9 nov. 2021 à 22:59, John Stone <johns_at_ks.uiuc.edu> a écrit :
>
>> 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/
>>
>