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 <nbigaoue...@gmail.com> 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 (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
