crossfade command not working from a command file
Hello, I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4. Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached). Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year). I would appreciate any help with this. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Guillaume, Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly. Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that. Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
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Hi Guillaume, Ok I fixed crossfade so it will work during movie recording when the graphics pane is not shown. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 Tom
On Sep 29, 2021, at 11:56 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Guillaume,
Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly.
Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that.
Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Great, thank you! So, it should also work when running everything from the shell ($ chimerax command-file.cxc), right? That would be ideal, since I like having a quit command at the end of the command file (not included in my example), allowing me to run it all from the shell and get my shell prompt back when the chimerax terminates. Guillaume On 30 Sep 2021, at 00:31, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: Hi Guillaume, Ok I fixed crossfade so it will work during movie recording when the graphics pane is not shown. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 Tom
On Sep 29, 2021, at 11:56 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Guillaume,
Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly.
Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that.
Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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<command-file.cxc><correct-result.mp4><wrong-result.mp4>
Yes I just tested and it runs from the shell with quit command at end of the file and saves the movie with correct crossfading. Tom
On Sep 30, 2021, at 3:03 AM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se> wrote:
Great, thank you! So, it should also work when running everything from the shell ($ chimerax command-file.cxc), right? That would be ideal, since I like having a quit command at the end of the command file (not included in my example), allowing me to run it all from the shell and get my shell prompt back when the chimerax terminates.
Guillaume
On 30 Sep 2021, at 00:31, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Guillaume,
Ok I fixed crossfade so it will work during movie recording when the graphics pane is not shown.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311>
Tom
On Sep 29, 2021, at 11:56 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Guillaume,
Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly.
Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that.
Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
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<command-file.cxc><correct-result.mp4><wrong-result.mp4>
Instead of putting a quit/exit command in your script, I recommend using the --exit option to ChimeraX. That will cause ChimeraX to exit after the command line arguments are processed. For example: chimerax --exit commands.cxc That has the advantage of not doing any of the web checks for newer versions of ChimeraX or bundles, so there won't be any extra popup dialogs or log output. And it let's you use commands.cxc in an interactive session without it causing ChimeraX to quit. It's a small tweak that isn't necessary, but you might like it. -- Greg On 9/30/2021 5:20 PM, Tom Goddard via ChimeraX-users wrote:
Yes I just tested and it runs from the shell with quit command at end of the file and saves the movie with correct crossfading.
Tom
On Sep 30, 2021, at 3:03 AM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se <mailto:guillaume.gaullier@icm.uu.se>> wrote:
Great, thank you! So, it should also work when running everything from the shell ($ chimerax command-file.cxc), right? That would be ideal, since I like having a quit command at the end of the command file (not included in my example), allowing me to run it all from the shell and get my shell prompt back when the chimerax terminates.
Guillaume
On 30 Sep 2021, at 00:31, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Guillaume,
Ok I fixed crossfade so it will work during movie recording when the graphics pane is not shown.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311>
Tom
On Sep 29, 2021, at 11:56 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Guillaume,
Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly.
Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that.
Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här:http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here:http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
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<command-file.cxc><correct-result.mp4><wrong-result.mp4>
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Excellent advice, thank you! And thank you Tom for testing this use case. Guillaume On 1 Oct 2021, at 02:43, Greg Couch via ChimeraX-users <ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu>> wrote: Instead of putting a quit/exit command in your script, I recommend using the --exit option to ChimeraX. That will cause ChimeraX to exit after the command line arguments are processed. For example: chimerax --exit commands.cxc That has the advantage of not doing any of the web checks for newer versions of ChimeraX or bundles, so there won't be any extra popup dialogs or log output. And it let's you use commands.cxc in an interactive session without it causing ChimeraX to quit. It's a small tweak that isn't necessary, but you might like it. -- Greg On 9/30/2021 5:20 PM, Tom Goddard via ChimeraX-users wrote: Yes I just tested and it runs from the shell with quit command at end of the file and saves the movie with correct crossfading. Tom On Sep 30, 2021, at 3:03 AM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se<mailto:guillaume.gaullier@icm.uu.se>> wrote: Great, thank you! So, it should also work when running everything from the shell ($ chimerax command-file.cxc), right? That would be ideal, since I like having a quit command at the end of the command file (not included in my example), allowing me to run it all from the shell and get my shell prompt back when the chimerax terminates. Guillaume On 30 Sep 2021, at 00:31, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: Hi Guillaume, Ok I fixed crossfade so it will work during movie recording when the graphics pane is not shown. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 Tom
On Sep 29, 2021, at 11:56 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Guillaume,
Thanks for the complete command script that demonstrates the problem. From the wrong movie I can see that it crossfades from entirely black to the intended image. In testing I find that it fades from entirely black (actually in my test it was solid red) because when the crossfade command is run it grabs the current image being shown in the graphics on screen, then fades that to the next rendered image. But if you have the file history thumbnails displayed where the graphics is normally, then the apparently graphics was not rendered to the screen and crossfade gets all black. If you hide the file history thumbnails before you open your script (use the Recent Files toolbar icon, or the lighting bolt icon in the lower right corner of main window), then the movie records correctly.
Usually the file history thumbnails are hidden automatically when the first model is opened. I will have to look at why that is not happening when opening a script. I will make a bug report and see if I can fix that.
Tom
On Sep 29, 2021, at 2:02 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4.
Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached).
Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year).
I would appreciate any help with this. Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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<command-file.cxc><correct-result.mp4><wrong-result.mp4> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Greg Couch -
Guillaume Gaullier -
Tom Goddard