Re: [PyMOL] Distance measure between pseudo atoms does not update over states

[Jarrett J. <jar...@sc...>]

Hi Istvan,

I can reproduce the same issue. Seems to be some unintended behavior with
how this multistate pseudoatom object is created. I've attached a modified
center_of_mass.py script so that it should behave the way you expect. Let
me know if this works for you.

Example that I tried with this:

fetch 1nmr
run center_of_mass_states_joined.py
com 1nmr, object=COM
wizard distance
# created distances between traj atom and pseudoatom

Hope that helps,
Jarrett J.

On Tue, Jul 18, 2023 at 12:52 PM Istvan Kolossvary <iko...@gm...>
wrote:

> 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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-- 

*Jarrett Johnson* | Senior Developer, PyMOL