Re: [PyMOL] Pymol 3 Timeline issues
Hi Jarrett, I feel it is easy enough for you to test in the scripting mode that whether "cmd.movie.produce(moviename,mode='ray',quality=85,quiet=0)" would produce the same with pymol3 and pymol2 after you load a 1000-frame dcd file to an object with load_traj. If not, do you have any suggestions how to let pymol3 behave like pymol2? Of course, I can always switch back to use pymol2, like I am doing now. Thanks, Lei On Sat, Jul 20, 2024 at 9:47 PM Jarrett Johnson < [email protected]> wrote: > 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 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 >> 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/[email protected] >>> Unsubscribe: >>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/[email protected] >> 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/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol 3 Timeline issues
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 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 > 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/[email protected] >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/[email protected] > 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/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol 3 Timeline issues
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 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/[email protected] > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] 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/[email protected] > 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/[email protected] 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 < [email protected]> 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/[email protected] >> 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/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
