[Chimera-users] surface transparency animation

Elaine Meng meng at cgl.ucsf.edu
Fri May 12 10:51:49 PDT 2017

Hi Lothar,
The “scolor” command does the coloring in a custom mode that is decoupled from the atoms and their patches.  The transparency command acts on the per-atom surface patches and so the scolor-colored surface is nonresponsive.  This may be a bug…. however, just use “color” to color the surface instead of “scolor" to avoid the problem, for example:

color green,s #0

(By the way, I don’t see any missing example on that page; there are two example commands each with an explanation under it.  Maybe you were expecting the example command to come after the explanation.)

Then you could make the surface transparent and gradually transition to opaque, for example:

transp 80,s #0; transp 0,s #0 frames 50

And to act on atomic patches of the surface you would just make a narrower specification than #0 including the residue numbers and maybe atom names.

I don’t think we ever noticed this issue before because single-color coloring with “scolor" is somewhat obscure and rarely used.  Sorry for the difficulty!  I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 12, 2017, at 10:26 AM, esserlo at helix.nih.gov wrote:
> Hi,
>  I am trying to animate a transition of a surface from 100% transparent to
> opaque.
> In a test (the real case is more complicated) I did this:
> open 1hen.pdb   # Lysozyme test
> # Chimera shows a blue ribbon model on gray background
> surface #0
> scolor #0 color green
> # chimera shows a green surface over a (now invisible) blue ribbon model
> # According to the manual the following (I think) should work:
> transparency 80,s #0
> # I expected to see the green surface to become 80% transparent and the blue
> ribbon model to shine through.
> # No luck. What am I missing ?
> BTW the page
> https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/transparency.html
> seems to be missing the last example concerning transparency of surface patches.
> Thanks,
>  Lothar

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