[chimerax-users] ChimeraX movie script tips

[Elaine Meng]

Hi Nicco,
That's a pretty good start!  It always takes a lot of trial and error to make a complicated movie script.  I CC'd the chimerax-users at cgl.ucsf.edu list (recommended for asking ChimeraX questions) but did not include your detailed script in case you wanted to keep it private.

ChimeraX does not automatically wait until each command is done before starting the next, so perhaps it is racing ahead to the encoding while previous commands are still executing.

It's always a little confusing (at least to me) when a "wait" command is needed, so when there seems to be missing content I usually just keep adding "; wait"  at the end of each line or to be even more sure,  "; wait N"  (where N is number of frames) after any multi-frame commands.

I suspect you need more wait commands in the last part of your script, say after the last H-bond calculation and/or the two last turn commands.

Other tips for your movie:

(1) The soft lighting isn't great for ribbons and sticks, it makes them look smudgy or sooty.  It is mainly for surfaces/space-filling displays.  Instead "light simple" or even "light gentle" may look better.

(2) in some cases you can avoid making selections and simply instead name the set of atoms and then use the name in the commands.  For example, instead of this

select /E:9-28 /E:32-39
show sel atoms
hbonds sel
select clear

... you could have this

name myres /E:9-28,32-39
show myres atoms
hbonds myres

(3) you can gradually restore a view over a number of frames instead of abrupt transition, for example, instead of 

view side; wait
view hole

... you could transition gradually over 60 frames with

view side; wait
view hole frames 60; wait 60

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 5, 2020, at 11:27 AM, Nicco <arecco.niccolo at gmail.com> wrote:
> 
> The following bug report has been submitted:
> Platform:        Darwin-19.3.0-x86_64-i386-64bit
> ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
> Description
> Hi,
> 
> I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called.
> 
> For example these commands below are not present in the movie but the movie encode is called afterwards. 
> # Select last interaction area
> select /F:370,375 /E:270,309,314
> show sel atoms 
> hbonds sel
> select clear
> 
> # Final show 
> turn x 15 60 rock 130
> turn -y 15 60 rock 130
> 
> I'm a bit puzzled of why this is happening and I don't really now how to fix it.
> 
> I attach the .cxc file with the set of instructions that I use to create the movie.
> Please consider that my experience level is beginner so there could be something that I'm doing wrong.
> 
> Thank you!
> Nicco
>