[Chimera-users] sphere transparency

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 12 10:50:09 PDT 2017


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 at 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




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