[Chimera-users] Surface Transparency Command Issues

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 28 10:20:54 PST 2014

Hi Josh,
I really can't tell from that description.  If you can provide a series of commands that demonstrates the problem (or a session at the point when you try the command + the exact command you then tried), you could use Help… Report a Bug and put that in the description field and/or attach the session file.  Be sure to include your email address if you want a response. 

The only vague idea I had is that maybe there are multiple transparent layers but have single-layer transparency turned on, which would only show the topmost transparent layer (and not any additional transparent things below it)… but it doesn't make any sense to me that the Actions… Surface menu would work (or did you mean to say that it didn't work??) and the command wouldn't.  Single-layer vs. multi-layer transparency can be toggled with the command "set singleLayer" / "~set singleLayer" (or in the Effects tool), but again, I'm skeptical that that is the issue.

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 27, 2014, at 11:32 PM, Joshua Carter <carter_jjc at hotmail.com> wrote:

> Hello,
> I'm having trouble getting the surface transparency command to work correctly.  I'm currently making a movie about the formation of a protein complex and I want the subunits to be shown as ribbons while they dock and then after they dock the electrostatic surface to appear.  I have the script written and the surface generated but when I use either the surftransp or transparency command nothing happens.  The command is correct, if I use it to change the transparency of a ribbon or atom it does so, but if I try to make the surface appear after docking nothing changes.  In addition, if I go to the Actions menu and change the surface transparency from there it also works.
> If you could help me figure out why the command won't work that would be extremely helpful.
> Thanks,
> Josh

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