[Chimera-users] DNA ladder different color than backbone

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 24 14:11:50 PDT 2015

Dear Belle,
At least according to my experiments, the ladder color is completely slaved to the ribbon color, and so (unfortunately) they always match.

There is a workaround, but it is rather tedious:

(1) open your structure, create your ribbon/ladder display in the color you want for the ladder rungs

(2) open another copy of the same structure, undisplay all of its atoms, and show only ribbons for that copy, in the color you want for the ribbons

(3) you will still see only the color of the first structure, must shrink the ribbons of the first copy so that they are inside the ribbons of the second copy

Example commands, other actions explained in brackets:

[start Chimera]
open 1bna
open 1bna
select #0

[start Nucleotides, e.g. menu: Actions… Atoms/Bonds… nucleotide objects… settings, then apply the desired ladder settings.  They will only apply to the first copy since #0 is selected and the “Restrict OK/Apply” option should be turned on.]
[start Ribbon Style Editor, e.g. menu: Tools… Depiction… Ribbon Style Editor.  Change Nucleic width and height values to something small like 0.05, apply.  Again, should only apply to first copy since #0 is selected and the “Restrict” option should be turned on]

[clear the selection if you don’t need it any more]

Now the two things will be in two different colors.  You can still change the colors, e.g. commands:

color hot pink #0
color yellow #1

Sorry it’s so tedious, there should be a simpler way.  I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 24, 2015, at 11:37 AM, Belle Lin <belle.lin at rcsb.org> wrote:
> Dear Chimera users/developers,
> Is there a way to make the DNA ladders a different color than the backbone? I am able to do so when the side (sugar/base) is shown in the "tube/slab" mode, but when I change it to the "ladder" mode I am unable to change the color of the rungs. I have included photos below which hopefully make my question more clear. Thank you in advance for your help!!
> Thanks,
> Belle Lin
> Able to create: 
> <image.png>
> <image.png>
> Trying to create: 
>  <image.png>

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