[chimerax-users] ChimeraX crossfade

[Tom Goddard]

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 at 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.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002703.html>
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002720.html <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 at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>>> On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867 at student.bham.ac.uk <mailto:DES867 at 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 at cgl.ucsf.edu <mailto:chimerax-users at 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 at cgl.ucsf.edu <mailto:chimerax-users at 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
>> 
>> 
>> 
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