Slight bug in ChimeraX
Hello!! My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs: 1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session. 2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following: graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr And these do not seem to run. Definitely not the lighting depthCue false. Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false. Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback. I am currently running ChimeraX-1.8-rc2024.05.10. Thank you guys!! Sergio. -- Sergio Pipaón Alcíbar (PhD Student) Dept. of Macromolecular Structures, lab. S0 / Ext: 5347 National Center for Biotechnology (CNB - CSIC) C/ Darwin, 3 28049, Cantoblanco-Madrid email: spipaon@cnb.csic.es
Hi Sergio! (1) I could not reproduce this problem. I tried both the 1.8 release and the current daily build. Started ChimeraX, opened a structure, turned off depth cueing, saved a session. Quit, restarted, restored session -- it does not have depth cueing turned on. You can just see it in the 3D window, or use "lighting" command with no arguments, which reports "depth cueing: 0" (meaning it is turned off). These sessions were saved with at least one model open. If you save an "empty" (no-models) session, it will be restored with depth cueing off, but the depth cueing may turn on automatically when you open the first model, see #2 below for more about that... (2) Actually your startup commands are applied (at least they were when I tried the same thing), but the lighting changes when you open the first model due to automatic styling. You can test this by starting up but NOT opening anything and using the "lighting" command without arguments - it reports "depth cue: 0" etc. as per your commands. However, as soon as you open the first model, with automatic styling the lighting may change. Automatic styling is described here: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> I didn't mention depth cueing in that page, but depth cueing is part of the "simple" lighting preset. You can avoid automatic styling by using "open" with the option "autostyle false" to open the first model in the session. For example, start the program, use command: open 2gbp autostyle false <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#options> However, it may be inconvenient without automatic styling because, for example, all the atoms will just be white spheres. So you may have to do a bunch of other commands to change display styles, colors, etc. So it might just be easier to open the first model (with all the autostyling), and then execute your commands after that. You can put your commands in a .cxc file and just open the .cxc file, or even make your own custom preset to put it in the menu so that you don't have to "manually" open the .cxc file. See custom presets, where you specify the .cxc file in the Startup section of Preferences: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 19, 2024, at 6:11 AM, Sergio Pipaón Alcíbar via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello!!
My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs:
1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session.
2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following:
graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr
And these do not seem to run. Definitely not the lighting depthCue false.
Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false.
Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback.
I am currently running ChimeraX-1.8-rc2024.05.10.
Thank you guys!!
Sergio.
Hi Sergio, You can use the OpenCommands <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxopencommands> bundle on the Toolshed (Tools→More Tools…) to run any command after a model is opened, so you could use it to turn depth cuing off after the autostyling has turned it on. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 19, 2024, at 11:02 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Sergio!
(1) I could not reproduce this problem. I tried both the 1.8 release and the current daily build. Started ChimeraX, opened a structure, turned off depth cueing, saved a session. Quit, restarted, restored session -- it does not have depth cueing turned on. You can just see it in the 3D window, or use "lighting" command with no arguments, which reports "depth cueing: 0" (meaning it is turned off).
These sessions were saved with at least one model open. If you save an "empty" (no-models) session, it will be restored with depth cueing off, but the depth cueing may turn on automatically when you open the first model, see #2 below for more about that...
(2) Actually your startup commands are applied (at least they were when I tried the same thing), but the lighting changes when you open the first model due to automatic styling. You can test this by starting up but NOT opening anything and using the "lighting" command without arguments - it reports "depth cue: 0" etc. as per your commands.
However, as soon as you open the first model, with automatic styling the lighting may change. Automatic styling is described here: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
I didn't mention depth cueing in that page, but depth cueing is part of the "simple" lighting preset.
You can avoid automatic styling by using "open" with the option "autostyle false" to open the first model in the session. For example, start the program, use command:
open 2gbp autostyle false
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#options>
However, it may be inconvenient without automatic styling because, for example, all the atoms will just be white spheres. So you may have to do a bunch of other commands to change display styles, colors, etc. So it might just be easier to open the first model (with all the autostyling), and then execute your commands after that. You can put your commands in a .cxc file and just open the .cxc file, or even make your own custom preset to put it in the menu so that you don't have to "manually" open the .cxc file.
See custom presets, where you specify the .cxc file in the Startup section of Preferences: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 19, 2024, at 6:11 AM, Sergio Pipaón Alcíbar via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello!!
My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs:
1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session.
2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following:
graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr
And these do not seem to run. Definitely not the lighting depthCue false.
Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false.
Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback.
I am currently running ChimeraX-1.8-rc2024.05.10.
Thank you guys!!
Sergio.
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Hi Sergio, As Elaine points out when you open the first atomic model in a ChimeraX session it sets "default" lighting with includes depth cue on. It does this as part of "auto-styling" where it sets how a molecule is initially displayed (ribbons, sticks, spheres, which atoms, ...). It enables "default" lighting when you open what it considers a small polymer, less than 5 chains and 200,000 atoms. Larger atomic models use full or soft lighting which does not enable depth cue. We don't have any good way to tell ChimeraX to redefine what it considers "default" lighting. But you could add a line to the ChimeraX Python code for the "lighting" command in your installation that would do that. On a Mac the file you would change is ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/std_commands/lighting.py and you would see lines if preset == 'default' or preset == 'simple': lp.shadows = False lp.multishadow = 0 sil.depth_jump = 0.03 lp.set_default_parameters(v.background_color) and you would add one line to that keeping the indentation if preset == 'default' or preset == 'simple': lp.shadows = False lp.multishadow = 0 sil.depth_jump = 0.03 lp.set_default_parameters(v.background_color) lp.depth_cue = False Then the ChimeraX default lighting command will always have depth cue off. Of course if you install a new ChimeraX you would have to change it again. When I try turning on and off depth cue in situations without clip planes it has such a minor effect I am surprised you even notice. When do you find depth cueing problematic? Tom
On Sep 19, 2024, at 6:11 AM, Sergio Pipaón Alcíbar via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello!!
My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs:
1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session.
2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following:
graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr
And these do not seem to run. Definitely not the lighting depthCue false.
Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false.
Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback.
I am currently running ChimeraX-1.8-rc2024.05.10.
Thank you guys!!
Sergio.
-- Sergio Pipaón Alcíbar (PhD Student) Dept. of Macromolecular Structures, lab. S0 / Ext: 5347 National Center for Biotechnology (CNB - CSIC) C/ Darwin, 3 28049, Cantoblanco-Madrid email: spipaon@cnb.csic.es
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participants (4)
-
Elaine Meng -
Eric Pettersen -
Sergio Pipaón Alcíbar -
Tom Goddard