Hi Haaris Ahsan Safdari, What command or steps did you use to make the protein transparent? I can only guess that they were incorrect somehow. I can't say any more without more details of what you did. It works fine for me in this example that I tried, commands and attached image of result: open 2gbp color lime color ligand yellow style ligand ball clashes sel restrict cross distanceOnly 3.5 ignoreHiddenModels true select true makePseudobonds false reveal true color sel & protein red ~sel transparency protein 50 target ar See command help pages for details, e.g. if you only want atoms and not ribbon transparent it would be "target a" instead of "target ar" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 12, 2023, at 2:05 AM, Haaris Ahsan Safdari via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX team,
I am working on a protein that clashes with RNA. Hence, to show those, I selected atoms of proteins (sphere representation) which are less or equal to 3.5Å from RNA and then colored them red. Through this criteria, some atoms of protein which do not clash with RNA, I keep them as lime colour. All of this works fine. Now, I wanted to show the clash more clearly since RNA segments pierces through many atoms of protein, so I wanted to make protein atoms (which is now a combination of red for clashing atoms and lime for non-clashing atoms) transparent.
However, as soon as I make my protein more transparent (by changing opacity), all atoms of my protein turn red and I lose the green ones which I dont want. I just wanted to know if there is any workaround for this (to retain green while making everything more transparent) or if it is just a bug?
Best regards, Haaris Ahsan Safdari
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