[Chimera-users] surface transparency animation
meng at cgl.ucsf.edu
Fri May 12 14:08:25 PDT 2017
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:
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”.
> On May 12, 2017, at 1:35 PM, esserlo at helix.nih.gov wrote:
>> Hi Lothar,
>> The âscolorâ 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 bugâ¦. however, just use âcolorâ to color the surface
>> instead of âscolor" to avoid the problem, for example:
>> color green,s #0
> This works.
>> (By the way, I donât 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 donât think we ever noticed this issue before because single-color
>> coloring with âscolor" 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:
>>> I am trying to animate a transition of a surface from 100% transparent to
>>> 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
>>> seems to be missing the last example concerning transparency of surface
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