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.... seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar
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 ----- 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@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....
seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar
Hi,
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 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 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 ----- 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@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....
seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar
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@helix.nih.gov wrote:
Hi,
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 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 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 ----- 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@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....
seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar
participants (2)
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Elaine Meng -
esserlo＠helix.nih.gov