Hello Diana, I changed the subject line to something descriptive of the question. In ChimeraX you would have to open the structure twice, show one as sticks, and show the other copy as transparent sphere or ball. For example, commands to show residue 6 of PDB 1gcn: open 1gcn open 1gcn show :6 style #2 sphere transparency #2 50 atoms There are help pages for all the commands: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> You don't have to show all of the same atoms as sticks and spheres, you could just show any specific one or more, e.g,. continuing on from the commands above, hide #2 show #2:6@cz ...or if sphere is too big, you can show ball and adjust ball scale style #2 ball size #2 ballscale .5 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 Jan 27, 2025, at 7:47 AM, Diana Carolina Mayorga Gonzalez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Hope you are well. I would like to know if I can do these transparent bubbles in ChimeraX showing the atoms stick as well. If it is possible, could you help me with a small tutorial, please?
<image.png> Thank you so much in advance,
Diana Carolina Mayorga G PhD Student Yannick Doyon Lab Research Center - Université Laval Department of Reproduction, mother and youth health (RSME) Québec, Canada