[chimerax-users] crossfade command not working from a command file

Greg Couch gregc at cgl.ucsf.edu
Thu Sep 30 17:43:06 PDT 2021 

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 at icm.uu.se <mailto:guillaume.gaullier at 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 at sonic.net 
>>> <mailto:goddard at 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 at cgl.ucsf.edu <mailto:chimerax-users at 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 at cgl.ucsf.edu 
>>> <mailto:chimerax-users at 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/>
>>> >>
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>>> >>
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>>> <command-file.cxc><correct-result.mp4><wrong-result.mp4>
>>
>
>
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