Hi, I have a simulation trajectory loaded in Pymol and I want to display certain interatomic distances interactively. This works perfectly fine with normal atoms, I can see how these selected distances change over the course of the simulation using the wizard and playing the movie. However, it seems that this feature doesn't work with pseudo atoms. I defined a couple of center-of-mass pseudo atoms using this script http://www.pymolwiki.org/index.php/center_of_mass. The script creates separate objects corresponding to the different COMs and each COM object has the same number of states as the trajectory object. I can use the wizard, select the distances, which show on the display, but when I play the movie, the distance values are not updated while the pseudo atoms do move around. The first thing I figured was that maybe the COM objects should be merged in a single object. So, I did that but to no avail, the distances are not updated while I play the movie. I must be overlooking something, can you tell me why this is not working?
Thank you very much, Istvan
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