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 <ikolos...@gmail.com> 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 > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *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
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
