[PyMOL] Pymol 3 Timeline issues
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 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol 3 Timeline issues
Hi Jarrett, Thanks for the quick reply. I am using version 3.03 on Linux and Mac. No conda package is yet available, so these are the Schrödinger provided binaries. Ray Tracing definitely uses only a single CPU. Regarding the Draw problem, I have the example that I used in my coursework. Can you point me to a place where I can upload it to? I have the Pymol session and the Draw/Ray videos. The total size is ~440 MB. BTW, I thought that saving a session with an active Timeline would save the Timeline as well, but that doesn't seem to be the case as you can see when you open the session file. Many thanks, Istvan On Fri, Jul 19, 2024 at 6:19 PM Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Istvan, > > With regards to CPU ray tracing only running on a single core, that sounds > like a major regression; we haven't changed anything in regards to that so > I'll investigate. As for your first issue, do you have any examples that I > can inspect myself to see what the issue is? > > Jarrett J. > > On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary > 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 >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Create command with ranges of states
Hi, It seems that the Create command can only copy either a single state or all states but no ranges. The range option would be very useful in stitching together a trajectory from parts of other trajectories. This functionality is readily available in the Timeline, but AFAIK not available in Create. Right now the only solution seems to use a hugely inefficient loop copying a whole range state by state. Does anyone know a better solution? Thanks, Istvan ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol 3 Timeline issues
Hi Istvan, With regards to CPU ray tracing only running on a single core, that sounds like a major regression; we haven't changed anything in regards to that so I'll investigate. As for your first issue, do you have any examples that I can inspect myself to see what the issue is? Jarrett J. On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary 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 > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
