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: Inline image 3] [image: Inline image 2] Trying to create: [image: Inline image 1]
Sorry, there is currently no way to do that without changing the code. If you're up to it, you need to edit the CHIMERA/share/NucleicAcids/__init__.py file where CHIMERA is the directory where Chimera is installed. In that file, inside the ladder function ('def ladder' on line 1273), you will find a loop (at line 1330) where it first gets the color of each residue in the ladder:
r0color_kwds = _ribbon_color(r0) r1color_kwds = _ribbon_color(r1) and later there are two drawCylinder() calls.
The "fix" is to add two more lines after fetching the residue colors to override them with the color you want, so those two lines become:
r0color_kwds = _ribbon_color(r0) r1color_kwds = _ribbon_color(r1) r0color_kwds['color'] = (.2, .8, .2) r1color_kwds['color'] = r0color_kwds['color']
Where (.2, .8, .2) are the RGB values of the color you want. HTH, Greg On 7/24/2015 11:37 AM, Belle Lin 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: Inline image 3
Inline image 2
Trying to create: Inline image 1
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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>
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@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@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>
participants (3)
-
Belle Lin -
Elaine Meng -
Greg Couch