Thank you very much. That is exactly what I needed! Best, Matt ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 18, 2024 3:43 PM To: Matthew Bubak <Matthew-Bubak@omrf.org> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Fwd: ChimeraX Chain Transparency Hi Matt, The address for ChimeraX questions is chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> CC'd here, as mentioned in the "contact us" page: <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html<https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>> Yes, of course you can make some of the atoms transparent and others not. I say "atoms" because at least in your image, you are displaying the atoms in the sphere style. You just need to specify that set of atoms in the transparency command, for example, for atoms of B chain only to be 70% transparent: transparency /B 70 target a ...or you could use menu: Select... Chains... [choose the one that you want] ...and then use command: transparency sel 70 target a The "target a" part means atoms. The default is to change transparency of only molecular surface (target s), so if you omit "target a" nothing happens to the atoms. Of course you can use a different % value than 70. 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 From: Matthew Bubak <Matthew-Bubak@omrf.org<mailto:Matthew-Bubak@omrf.org>> Subject: ChimeraX Chain Transparency Date: April 18, 2024 at 12:48:22 PM PDT Hello, I am trying to make specific chains of mitochondrial complexes more or less transparent. I am able to make the entier complex transparent, but not individual chains. For example in the figure below (mitochondrial complex I), I would like to make the purple chains approximately 50% transparent, and the blue chain 90% transperent, and leave the rest untouched. Is this possible? [cid:6eb881ac-78a9-431d-b81b-b093ec206550] Thank you for your help, Matt Bubak, PhD. Post-Doctoral Fellow Aging and Metabolism Program The Oklahoma Medical Research Foundation
