[Chimera-users] DNA ladder different color than backbone

Belle Lin belle.lin at rcsb.org
Sat Jul 25 19:31:37 PDT 2015


Thank you so much! Your instructions were extremely helpful and I was able
to successfully make the colors in the way I was hoping for :)

[image: Inline image 1]

On Fri, Jul 24, 2015 at 5:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> ~disp
> 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
> ----------
> 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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