Hi Nicolas, unset static_singletons
Cheers, -- Jason On Tue, Mar 8, 2011 at 10:21 AM, Nicolas Bigaouette <[email protected]> wrote: > Hi Jason, > > Thanks for your input. > > I've looked at the all_states option, but it was not set (or set to false). > If I explicitely set it to 1/true, I see every state of particles and boxes. > > To reproduce, I've created a small test script and uploaded it to github. > You can get it here: > https://github.com/nbigaouette/pymol_boxes > and clone it: > git clone git://github.com/nbigaouette/pymol_boxes.git > Then simply run with: > ./pymol_boxes.py > > Even though all information is located in the data files, I just plot box id > #121 for now. The white ball is traveling from right to left, and when it > leaves box #121, the box should disappear: it is not. If you disable the > check at line 44, all boxes will be drawn. The two smallest box appearing at > frame 22 of the animation disappear at frame 25. Box 121 is shown every > frame while it should disappear at frame 8. > > I think I've found the problem. If I add a box at frame 1 (the first one), > it will stay on forever! To verify this, I added a (commented) test at line > 43. If I skip t=0 (the first frame, note the t+1 send to > pymol_objects.DrawBox() at line 54), then box 121 will disappear when it > should (when the white particle is leaving it). If the box is added at the > first frame, it will stay there during the animation... > > Could that be a bug in pymol? Or is there still something I'm missing? > > I hope the example code will help out. > > Thanks a lot! > > Nicolas > > > On Mon, Mar 7, 2011 at 10:17 PM, Jason Vertrees > <[email protected]> wrote: >> >> Hi Nicolas, >> >> It sounds like you have the "all_states" option set. So, to only have >> one object state shown at a time, try >> >> unset all_states >> >> Also, deleting anything in PyMOL is easy: >> >> delete objName >> >> or through the cmd API: >> >> cmd.delete("objName") >> >> Cheers, >> >> -- Jason >> >> On Mon, Mar 7, 2011 at 9:11 PM, Nicolas Bigaouette >> <[email protected]> wrote: >> > Hi Jason, >> > >> > Thanks for your reply. No, I'm not deleting the cgo objects after the >> > relevant frames. Actualy, I don't know how. This what I wanted to do >> > though. >> > >> > I was able to achieve a workaround. Each time load_cgo() is called to >> > create >> > a box, a loop will go through all later time steps adding an empty cgo >> > object of the same name. But it seems to be really slow, as expected. >> > >> > So my error was thinking that giving an object a state would draw the >> > object >> > only at that frame: it seems it is drawn for all later frames. >> > >> > Thus, how can I add an object only for a given state/frame? Should I >> > delete >> > the object at the next state/frame? What would be the command to delete >> > a >> > cgo object? >> > >> > Should I store what load_cgo() returns and issue a "delete" over that >> > object? >> > >> > Thanks! >> > >> > >> > On Mon, Mar 7, 2011 at 9:03 PM, Jason Vertrees >> > <[email protected]> wrote: >> >> >> >> Hi Nicolas, >> >> >> >> Are you hiding or deleting the boxes after the relevant frame passes? >> >> This is hard to debug without seeing sample code. >> >> >> >> Cheers, >> >> >> >> -- Jason >> >> >> >> On Mon, Mar 7, 2011 at 8:39 PM, Nicolas Bigaouette >> >> <[email protected]> wrote: >> >> > Hi all, >> >> > >> >> > I'm usin pymol to vizualize my molecular dynamics code. Particle >> >> > positions >> >> > is saved in a single .xyz file. An example is: >> >> > 2 >> >> > 0.00000 fs -- MD of 2 particles (position in Angstrom) >> >> > A 0.000 0.000 0.000 >> >> > E 13.020 0.000 0.000 >> >> > 2 >> >> > 0.00050 fs -- MD of 2 particles (position in Angstrom) >> >> > A 0.000 0.000 0.000 >> >> > E 10.520 0.000 0.000 >> >> > [...] >> >> > The number "2" (appearing twice) gives the number of particles to be >> >> > read >> >> > for that time step. >> >> > >> >> > I want to add some boxes around some of the particles, so I wrote a a >> >> > function that creates a CGO object and add it to a frame/timestep >> >> > using >> >> > "cmd.load_cgo(my_cjo_obj,boxname,timestep)". >> >> > >> >> > For each time step of my simulation, I load the box informations from >> >> > a >> >> > file >> >> > and call my cgo-creating function for the boxes present in the file. >> >> > For >> >> > some time steps, a single box is drawn, for other time steps I can >> >> > have >> >> > many >> >> > of them. Some boxes can disappear and also re-appear at a later time >> >> > step. >> >> > >> >> > This means I have "duplicates" boxes. If a box is present at two >> >> > different >> >> > time steps (with the same "boxname" when calling load_cgo()), it will >> >> > be >> >> > created in pymol multiple times, but the "timestep" option of the >> >> > "load_cgo()" command should make it appear at the right time step. >> >> > >> >> > Unfortunately, it is not working as expected. All the boxes are drawn >> >> > correctly and they appear at the righ time. BUT, some of them are not >> >> > "hidden" (or deleted) when they should. >> >> > >> >> > As an example, I'm attaching a webm video of a particle travelling >> >> > from >> >> > right to left (white ball). The initial frame is correct: the boxes >> >> > are >> >> > correctly drawn where I want them. As the particle travels, boxes >> >> > should >> >> > adapt to its location. New boxes are created fine: as the particle is >> >> > traveling, we can see boxes adjusting around it. But the two smallest >> >> > boxes >> >> > are always shown while they should not appear starting from half of >> >> > the >> >> > movie. >> >> > >> >> > In the loop which creates the CGO objects, I print the box properties >> >> > to >> >> > verify that I don't add the two small boxes when they shouldn't >> >> > appear. >> >> > Except from that, I don't know what else could be wrong. Maybe I'm >> >> > abusing >> >> > the "state" argument to load_cgo() or not using it correctly? >> >> > >> >> > Thank you for any help! >> >> > >> >> > Nicolas >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > What You Don't Know About Data Connectivity CAN Hurt You >> >> > This paper provides an overview of data connectivity, details >> >> > its effect on application quality, and explores various alternative >> >> > solutions. http://p.sf.net/sfu/progress-d2d >> >> > _______________________________________________ >> >> > PyMOL-users mailing list ([email protected]) >> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > Archives: >> >> > http://www.mail-archive.com/[email protected] >> >> > >> >> >> >> >> >> >> >> -- >> >> Jason Vertrees, PhD >> >> PyMOL Product Manager >> >> Schrodinger, LLC >> >> >> >> (e) [email protected] >> >> (o) +1 (603) 374-7120 >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > What You Don't Know About Data Connectivity CAN Hurt You >> > This paper provides an overview of data connectivity, details >> > its effect on application quality, and explores various alternative >> > solutions. http://p.sf.net/sfu/progress-d2d >> > _______________________________________________ >> > PyMOL-users mailing list ([email protected]) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/[email protected] >> > >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 >> >> >> ------------------------------------------------------------------------------ >> What You Don't Know About Data Connectivity CAN Hurt You >> This paper provides an overview of data connectivity, details >> its effect on application quality, and explores various alternative >> solutions. http://p.sf.net/sfu/progress-d2d >> _______________________________________________ >> PyMOL-users mailing list ([email protected]) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/[email protected] > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
