[Chimera-users] surface transparency animation

esserlo at helix.nih.gov esserlo at helix.nih.gov
Fri May 12 13:35:59 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
  This works.

> (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.)

  You are right, all info is there indeed. Sorry.

> Then you could make the surface transparent and gradually transition to
> opaque, for example:
> transp 80,s #0; transp 0,s #0 frames 50

Yes it worked. Somehow I still mange get thoroughly confused about some syntax.

I needed to split my molecule and ended up with a very complicated animation
that worked but is rather awkward:

split #0 atoms :98-140.A atoms :98-140.B

So while I was rotating the ribbon model it got wrapped in a surface:

perframe "colordef tmx 1.0 0.5 0. $1; scolor #0.1 color tmx" range 0,1 frames 180

May I ask you how to break across the lines ? I had a perframe statement in
double quotes that was very very long due to lots of different colors and sub
surfaces. I would like to be able to break across the line. Should this work ?

perframe "colordef tmx 1.0 0.5 0.0 $1; \
          scolor #0.1 color tmx" range 0,1 frames 20

(Not tried yet).

But thanks with your above information I think I can greatly simplify this


> 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
> -----
> 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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