Dear Siyu Chen, I believe this is a bug, or at least a limitation of the "transparency" command. The "f" target is supposed to include nucleotide representations. I will make a bug-report ticket for this -- thanks for letting us know. It may not have been implemented yet, since I see that the "transparency" manual page does not list it currently: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> What works currently is the "color" command with target f, and you can include transparency in the color command. It is not as convenient if there are multiple colors, since you would need a separate color command for each color, instead of a single transparency command. However, in your case, it sounds like all the stubs are already the same color and you would be able to use a single command, for example: color nucleic cyan trans 50 targ f <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 16, 2020, at 12:43 PM, Siyu Chen <siyuchen2021@u.northwestern.edu> wrote:
Dear chimerax developers,
I am writing to ask about an issue regarding to the transparency of DNA bases.
I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue?
Thanks in advance for your time and help!
Best, Siyu Chen