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
boxes.webm
Description: video/webm
------------------------------------------------------------------------------ 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
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