Hi Tom, The broader command is simply “transparency” … it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a “frames” option for fading in/out over a specified number of frames. So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames: open 2gbp show :bgc repr sphere :bgc transp 100,a :bgc frames 100 … in this case “ligand” could be used instead of “:bgc” but I showed a more general case of specifying by residue name, since “ligand” doesn’t always get what you want. The “,a” means to affect atomic representations, not surfaces, ribbons, etc. See the manpage: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> The “surftransparency” manpage (e.g. shown with command “help surftransparency” refers to this “transparency” command which essentially replaces it, although surftransparency still works too. See also the movie-related commands list, including “coordset” to play through your morph. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> There is also a list of all commands, of course… <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … and you can also use "Help… Search Documentation” in the menu to search for specific terms like “transparency" I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk@brandeis.edu> wrote:
Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky