Join states

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Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.creating

join_states can combine multiple objects to a multi-state object. It's the reverse of split_states.

By default the input objects must be identical with respect to all atom identifiers. Atoms which are missing in any input object are skipped. If any identifier does not match (for example chain) you need discrete=-2 which will match atoms by sequence alignment.

This command has been integrated in PyMOL 1.7.2


join_states name [, selection [, discrete ]]


  • name = string: name of object to create or modify
  • selection = string: atoms to include in the new object {default: all}
  • discrete = integer
    • -2: match atoms by sequence alignment
    • -1: Assume identical input objects (matching all atom identifiers) but also check for missing atoms and only include atoms that are present in all input objects {default}
    • 0: Assume identical input objects
    • 1: Input object may be (totally) different


$ # launch pymol from terminal with all models from a modeller run
$ pymol foo.B9999*.pdb

PyMOL> # create multi-state model
PyMOL> join_states multifoo, foo*, 0
PyMOL> delete foo*
PyMOL> intra_fit multifoo

See Also