Re: [chimerax-users] ChimeraX crossfade
On Apr 27, 2022, at 9:43 AM, Daisy Sassoon DES867@student.bham.ac.uk wrote:
Hi Elaine, I hope you are well. I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. Do you have any advice?
My code is shown below: [... edited out by Elaine ...]
Many thanks, Daisy
Sent from Mail for Windows
Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively.
Unless you are including data that needs to remain private, it is best to send questions to chimerax-users@cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.)
I'm CC-ing chimerax-users@cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private.
However, here are some specific notes on the script:
(1) the "view 3" command causes an error so I had to comment it out of your script to try it
(2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text
(3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Daisy,
I remember I ran into a similar problem some time ago, and it was identified as a bug and fixed in a subsequent version of ChimeraX. See these messages:
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002703.htm... https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002720.htm...
So, I would suggest checking that you are using the latest version of ChimeraX.
I hope this helps,
Guillaume
On 27 Apr 2022, at 20:22, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867@student.bham.ac.ukmailto:DES867@student.bham.ac.uk> wrote:
Hi Elaine, I hope you are well. I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. Do you have any advice?
My code is shown below: [... edited out by Elaine ...]
Many thanks, Daisy
Sent from Mail for Windows
Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively.
Unless you are including data that needs to remain private, it is best to send questions to chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.)
I'm CC-ing chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private.
However, here are some specific notes on the script:
(1) the "view 3" command causes an error so I had to comment it out of your script to try it
(2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text
(3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Yeah there was a crossfade command problem when the file history thumbnails cover the graphics pane that was fixed in ChimeraX 1.3
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311
Thanks for reminding us of that issue.
Tom
On Apr 28, 2022, at 2:34 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Daisy,
I remember I ran into a similar problem some time ago, and it was identified as a bug and fixed in a subsequent version of ChimeraX. See these messages:
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002703.htm... https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002703.html https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002720.htm... https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002720.html
So, I would suggest checking that you are using the latest version of ChimeraX.
I hope this helps,
Guillaume
On 27 Apr 2022, at 20:22, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867@student.bham.ac.uk mailto:DES867@student.bham.ac.uk> wrote:
Hi Elaine, I hope you are well. I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. Do you have any advice?
My code is shown below: [... edited out by Elaine ...]
Many thanks, Daisy
Sent from Mail for Windows
Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively.
Unless you are including data that needs to remain private, it is best to send questions to chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.)
I'm CC-ing chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private.
However, here are some specific notes on the script:
(1) the "view 3" command causes an error so I had to comment it out of your script to try it
(2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text
(3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade>
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
participants (3)
-
Elaine Meng -
Guillaume Gaullier -
Tom Goddard