VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 19 2020 - 14:38:45 CDT

Hi,
  If you use the "user" field to assign your cluster index, you can map
up to 1024 distinct colors, and since the color scales can be programmed
with custom colors of your choosing, this should be well more than what
you need. I've attached an example script that contains a bunc of
procs that can reprogram the VMD color scales to color scales found in
Matlab and similar programs as an example of how to set the color scale
colors to anything you like. By using the custom color scale,
"Color by User", and setting the color scale data range appropriately,
you can achieve a very broad range of possibilities for any number of
unique colors up to 1024.

Best regards,
  John Stone

On Sun, Oct 18, 2020 at 04:07:25PM +0530, Remya Ann wrote:
> Hi Doa'a,
> Yes I changed the color scale. But I don't have enough colorid options to
> name all 50 clusters. (My cluster 1 has particle name h1 and cluster 50
> has particle name h50)
> As mentioned earlier after colorid 32 i have to go back again to colorid
> 0...and changing the color scale of this is changing the previously
> assigned colordid 0 too..
> Hope I'm able to express myself clearly.
> Regards,
> Remya
>
> On Sun, 18 Oct 2020, 15:43 Dr. Doa'a, <[1]doaa.saayed_at_gmail.com> wrote:
>
> Hi Remya,
> Did you try changing the color scale?
> This way you can choose the intensity of the color and thus you can
> distinguish all your clusters.
> On Sun, 18 Oct 2020 at 11:02, Remya Ann <[2]remya.mathewskl_at_gmail.com>
> wrote:
>
> Hi thanks for the link Ashar.
> But my problem is that there are only 33 options for colors names in
> the repesentations->coloring method tab. Which I assign to first 33
> clusters. If my first cluster is assigned colorid0, then 34th cluster
> is again assigned colorid0 and I try to adjust the colormap to vary
> the color. But this also causes a change in the color of the first
> cluster as well. So is there a way to create more options for the
> color names itself.
> It would really be helpful if some one can help me with this.
> Thanks and Regards,
> Remya
> On Sun, 18 Oct 2020 at 08:53, Ashar Malik <[3]asharjm_at_gmail.com>
> wrote:
>
> Have you had a look at this:Â
> [4]https://www.ks.uiuc.edu/Research/vmd/current/ug/node83.html#ug:topic:coloring
> On Sun, Oct 18, 2020 at 3:13 AM Remya Ann
> <[5]remya.mathewskl_at_gmail.com> wrote:
>
> Hi,
> Is there a way to get more colors than the 32 colors mentioned in
> the colors tab and representation tab in the graphics tab in
> VMD.
> I have around 50 clusters of particles in a frame and would like
> to give a different color to each cluster.
> Any help would be appreciated.
> Thanks and Regards,
> --
> Remya Ann Mathews K
> Doctoral Scholar
> Polymer Engineering and Colloid Science Lab
> Department of Chemical Engineering
> Indian Institute of Technology Madras
> Chennai - 600 036, TamilNadu, India
>
> --
> Remya Ann Mathews K
> Doctoral Scholar
> Polymer Engineering and Colloid Science Lab
> Department of Chemical Engineering
> Indian Institute of Technology Madras
> Chennai - 600 036, TamilNadu, India
>
> --
> Doa'a
> Physical Chemistry PhD student at Tehran University
>
> References
>
> Visible links
> 1. mailto:doaa.saayed_at_gmail.com
> 2. mailto:remya.mathewskl_at_gmail.com
> 3. mailto:asharjm_at_gmail.com
> 4. https://www.ks.uiuc.edu/Research/vmd/current/ug/node83.html#ug:topic:coloring
> 5. mailto:remya.mathewskl_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/