Re: [PyMOL] Pymol 3 Timeline issues

[Jarrett J. <jar...@sc...>]

Hi Lei,

I may need more details on how you're producing your movies. I would note
that the File menu will only produce a movie based on the movie that's in
the timeline *not* the one from PyMOL 2. So if you're using the old movie
API to export out a movie in PyMOL 3, your results won't be as expected
unless you use the legacy export menu. The `load_traj` command, I believe,
was unchanged moving to PyMOL3, if you can provide more details on what has
changed for you, that'd be great. While the interface is improved in
PyMOL3, I've also made sure to accommodate for most use cases of the
Timeline to be configured via scripting. The Python API for it is located
here: https://pymolwiki.org/index.php/Timeline_Python_API.

Jarrett J

On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote:

> Hi Istvan,
>
> I have related but not the same problems with pymol3 when making the
> movies. Using the pymol script that works for pymol 2.5, pymol3 could only
> produce a movie for the first 240(?) frames and I could not find the
> setting to fix this issue. In addition, I believe they also changed the
> default options of load_traj in pymol3. Overall, it appears pymol3 counts
> on you using the interface but this is not always ideal for heavy duty
> work, e.g., requiring running "pymol -c" (text mode) on a linux server to
> finish the job.
>
> Lei
>
>
>
> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
> wrote:
>
>> Hi,
>>
>> I have had these issues with the new timeline. It works fine with scenes
>> and short multi-state objects (like those showcased in the Pymol 3 online
>> visualization course) but when it comes to real life MD trajectories I
>> found two "dealbreaker" issues.
>>
>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>> mode is not working. If I select Draw to generate a movie file quickly for
>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>> is complete garbage, showing only random parts of the system.
>>
>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>> automatically uses all the available cores for ray tracing. The way Pymol 3
>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>> only 100 seconds.
>>
>> Has anyone encountered similar issues?
>>
>> Thanks,
>>
>>    Istvan
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-- 

*Jarrett Johnson* | Senior Developer, PyMOL