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
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
'''
See more here: http://www.pymolwiki.org/index.php/center_of_mass
DESCRIPTION
Places a pseudoatom at the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
SEE ALSO
pseudoatom, get_com
'''
from __future__ import print_function
from pymol import cmd
def com(selection, state=None, mass=None, object=None, quiet=1, **kwargs):
quiet = int(quiet)
if (object == None):
try:
object = cmd.get_legal_name(selection)
object = cmd.get_unused_name(object + "_COM", 0)
except AttributeError:
object = 'COM'
cmd.delete(object)
if (state != None):
x, y, z = get_com(selection, mass=mass, quiet=quiet)
if not quiet:
print("%f %f %f" % (x, y, z))
cmd.pseudoatom(object, pos=[x, y, z], **kwargs)
cmd.show("spheres", object)
else:
for i in range(cmd.count_states()):
x, y, z = get_com(selection, mass=mass, state=i + 1, quiet=quiet)
if not quiet:
print("State %d:%f %f %f" % (i + 1, x, y, z))
obj_name = f"_COM{object}{i}"
cmd.pseudoatom(obj_name, pos=[x, y, z], **kwargs)
cmd.show("spheres", 'last ' + obj_name)
cmd.join_states(object, f"_COM{object}*")
cmd.delete(f"_COM{object}*")
cmd.extend("com", com)
def get_com(selection, state=1, mass=None, quiet=1):
"""
DESCRIPTION
Calculates the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
"""
quiet = int(quiet)
totmass = 0.0
if mass != None and not quiet:
print("Calculating mass-weighted COM")
state = int(state)
model = cmd.get_model(selection, state)
x, y, z = 0, 0, 0
for a in model.atom:
if (mass != None):
m = a.get_mass()
x += a.coord[0] * m
y += a.coord[1] * m
z += a.coord[2] * m
totmass += m
else:
x += a.coord[0]
y += a.coord[1]
z += a.coord[2]
if (mass != None):
return x / totmass, y / totmass, z / totmass
else:
return x / len(model.atom), y / len(model.atom), z / len(model.atom)
cmd.extend("get_com", get_com)
# vi:expandtab:sw=3
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