From: Bart Bruininks (
Date: Thu Jun 27 2019 - 10:05:11 CDT


I am currently working on some cool clustering scripts and what I would
like to do is show the clustering in VMD. However, to do so, I need to be
able to make an adaptive selection based on a full trajectory spanning
cluster array (numpy) per atom e.g.:

  [frame 1
    atom1 1
    atom2 3
    atom3 1
  . ..
  [frame 2
    atom1 1
    atom2 2

I would like to use the atom clusters per frame as my selection and color
them based on cluster name. However, this seems to be more complex then I
had hoped. I do know some tcl etc so I could figure it out, I am just
wondering what would be a wise path to take.


Bart Bruininks
MD Groningen (Martini)