Hi Woo-Ri Shin, This command works fine for me. Remember, the alias only creates the command. Then, you still have to actually use the new command for anything to happen. These commands including your modified alias work correctly for me: open 1bna alias nucrib cartoon style /A xsect oval width 1.6 thick 1.6 nucrib However, it does not make sense to put "/A" in the alias. You cannot have different cartoon styles in the same model based on chain IDs. So in the example above, both chains /A and /B get the new style. However, you can have different for nucleic vs. protein, so it would make more sense for you to use the alias as it was in my original example: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> These commands with my example alias work correctly to change only the style of the nucleic-acid ribbon: open 1tro style stick cartoon alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6 nucrib For the protein + nucleic acid situation as in 1tro, my example works correctly to change only the nucleic acid ribbon, and also as shown in the image from the help page that you attached. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 5, 2024, at 10:26 PM, Woo-Ri Shin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi I have a question about making images for protein-DNA(or RNA) complex structures. I want to make the round shape of DNA (or RNA) backbone using "nucrib" command which is provided on the web (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html). But this command doesn't work. I have the docking structure including RNA of chain A and protein of chain B. So then I modified the command like this: alias nucrib cartoon style /A xsect oval width 1.6 thick 1.6
This command doesn't work and still initial cartoon style. Could you check this problem? <image.png> Thank you
Best, Woo-Ri Shin -- Woo-Ri Shin, Ph.D.
Department of Bioengineering University of Pennsylvania E-mail: wr1203@seas.upenn.edu Phone: +1 (267)213-2572