[Chimera-users] surface transparency animation

Elaine Meng meng at cgl.ucsf.edu
Fri May 12 14:08:25 PDT 2017


Hi Lothar,
Sorry, I don’t know a way to specify line breaks in command files, nor do I know how long a line can be before there are problems.  It might depend on the platform.

All I know about command file contents is summarized here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>

Maybe you already “got” this point, but for your example perframe command it would be a lot simpler to just use the transparency command with a frames argument, after coloring the surface with “color” rather than “scolor”.
Best,
Elaine

> On May 12, 2017, at 1:35 PM, esserlo at helix.nih.gov wrote:
> 
> Hi,
> 
>> 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
> animation.
> 
> Lothar
> 
> 
>> 
>> 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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