[chimerax-users] ChimeraX movie script tips

[Elaine Meng]

Hi Nicco,
Yes, we recommend using that e-mail address for ChimeraX questions and suggestions, unless you need to include some information that needs to be kept private.  You can sign up to be a member of the list (see link below) to send questions instantly and see other people's messages, or even if you are not a member, send questions with slight delay for approval by the moderator.

If you get a bug/error, however, it is better to use the menu: Help... Report a Bug.  

The ways to contact us are described on this page:

<http://www.rbvi.ucsf.edu/chimerax/docs/contact.html>

You don't need to also CC me, I'm already on that list along with the other developers.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 8, 2020, at 7:09 AM, Niccolò Arecco <arecco.niccolo at gmail.com> wrote:
> 
> Hi Elaine,
> 
> OMG! Thanks you so much! 
> Adding 2 waits at the end of the script solved my issue! 
> Also thanks for the other professional tips, especially lighting and moving are so much nicer!
> 
> So in the future it is better to write to chimerax-users at cgl.ucsf.edu for any issue I should encounter?
> 
> Thanks a lot!
> Nicco
> 
>> On 6 Jul 2020, at 23:08, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> 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