Surface caps only colored interactively
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong? view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true Best, -da
Hi Daniel, Put a "wait 1" command after the "view front.cut" command. Cryptic, I know! The trouble is that when running a script the graphics is never redrawn unless you use this "wait" command which says to draw a frame. The cap is not computed unless the graphics is redrawn. So the coloring happens before the cap is computed unless you use this wait command. In Chimera running scripts redraws between each line of the script, but this slows down running the script so we are trying not doing those redraws in ChimeraX. But this case and a few others (like changing map contouring level) only cause updates to the surfaces when the frames are redrawn. We need to figure out a better compromise between speed and obvious behavior. Tom
On Apr 7, 2021, at 6:27 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong?
view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks! I actually tried "wait" but not "wait 1," but I guess the calling wait without a number of frames is really a special case for commands like turn. -da On Wed, Apr 7, 2021 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Put a "wait 1" command after the "view front.cut" command. Cryptic, I know!
The trouble is that when running a script the graphics is never redrawn unless you use this "wait" command which says to draw a frame. The cap is not computed unless the graphics is redrawn. So the coloring happens before the cap is computed unless you use this wait command.
In Chimera running scripts redraws between each line of the script, but this slows down running the script so we are trying not doing those redraws in ChimeraX. But this case and a few others (like changing map contouring level) only cause updates to the surfaces when the frames are redrawn. We need to figure out a better compromise between speed and obvious behavior.
Tom
On Apr 7, 2021, at 6:27 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong?
view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Yep. Using "wait" without specifying a number of frames means wait until any ongoing model motion has stopped. There is no motion in this case so no frames get drawn. I now recall what we did to make sure these wait commands are not needed for map contour level changes -- ChimeraX updates the map surface immediately if it is running in a script. I will try to make the clip caps also update immediately when created in a script. Tom
On Apr 7, 2021, at 6:40 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Thanks! I actually tried "wait" but not "wait 1," but I guess the calling wait without a number of frames is really a special case for commands like turn.
-da
On Wed, Apr 7, 2021 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Put a "wait 1" command after the "view front.cut" command. Cryptic, I know!
The trouble is that when running a script the graphics is never redrawn unless you use this "wait" command which says to draw a frame. The cap is not computed unless the graphics is redrawn. So the coloring happens before the cap is computed unless you use this wait command.
In Chimera running scripts redraws between each line of the script, but this slows down running the script so we are trying not doing those redraws in ChimeraX. But this case and a few others (like changing map contouring level) only cause updates to the surfaces when the frames are redrawn. We need to figure out a better compromise between speed and obvious behavior.
Tom
On Apr 7, 2021, at 6:27 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong?
view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Awesome, thanks! Best, -da On Wed, Apr 7, 2021 at 6:45 PM Tom Goddard <goddard@sonic.net> wrote:
Yep. Using "wait" without specifying a number of frames means wait until any ongoing model motion has stopped. There is no motion in this case so no frames get drawn.
I now recall what we did to make sure these wait commands are not needed for map contour level changes -- ChimeraX updates the map surface immediately if it is running in a script. I will try to make the clip caps also update immediately when created in a script.
Tom
On Apr 7, 2021, at 6:40 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Thanks! I actually tried "wait" but not "wait 1," but I guess the calling wait without a number of frames is really a special case for commands like turn.
-da
On Wed, Apr 7, 2021 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Put a "wait 1" command after the "view front.cut" command. Cryptic, I know!
The trouble is that when running a script the graphics is never redrawn unless you use this "wait" command which says to draw a frame. The cap is not computed unless the graphics is redrawn. So the coloring happens before the cap is computed unless you use this wait command.
In Chimera running scripts redraws between each line of the script, but this slows down running the script so we are trying not doing those redraws in ChimeraX. But this case and a few others (like changing map contouring level) only cause updates to the surfaces when the frames are redrawn. We need to figure out a better compromise between speed and obvious behavior.
Tom
On Apr 7, 2021, at 6:27 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong?
view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I made the view and clip commands update the clip cap surfaces immediately so that the "wait 1" command in your ChimeraX script will no longer be needed to get the cap coloring to work. This will be in tomorrow's daily build and in ChimeraX 1.2 which we plan to release at the end of the month. Tom
On Apr 7, 2021, at 6:45 PM, Tom Goddard <goddard@sonic.net> wrote:
Yep. Using "wait" without specifying a number of frames means wait until any ongoing model motion has stopped. There is no motion in this case so no frames get drawn.
I now recall what we did to make sure these wait commands are not needed for map contour level changes -- ChimeraX updates the map surface immediately if it is running in a script. I will try to make the clip caps also update immediately when created in a script.
Tom
On Apr 7, 2021, at 6:40 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Thanks! I actually tried "wait" but not "wait 1," but I guess the calling wait without a number of frames is really a special case for commands like turn.
-da
On Wed, Apr 7, 2021 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Put a "wait 1" command after the "view front.cut" command. Cryptic, I know!
The trouble is that when running a script the graphics is never redrawn unless you use this "wait" command which says to draw a frame. The cap is not computed unless the graphics is redrawn. So the coloring happens before the cap is computed unless you use this wait command.
In Chimera running scripts redraws between each line of the script, but this slows down running the script so we are trying not doing those redraws in ChimeraX. But this case and a few others (like changing map contouring level) only cause updates to the surfaces when the frames are redrawn. We need to figure out a better compromise between speed and obvious behavior.
Tom
On Apr 7, 2021, at 6:27 PM, Daniel Asarnow <asarnow@msg.ucsf.edu> wrote:
Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong?
view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Daniel Asarnow -
Tom Goddard