[Chimera-users] Reading Chimera source ...?

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 17 16:45:04 PST 2014

On Nov 17, 2014, at 4:26 PM, Boris Steipe <boris.steipe at utoronto.ca> wrote:

>>> For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects.

If we are talking about the the 'sel' argument given to many of the functions in Midas/__init__.py, that argument is usually "polymorphic", and can be any one of these:

  -- an atom specifier (e.g. "#1 at ca")
  -- a list/tuple of Atoms/Residues/Molecules (homogeneous list/tuple though)
  -- a set of Atoms/Residues/Molecules (also homogenous, and unlike the list/tuple the set has to be at the right "level" for the function called [e.g. Atoms for distance])
  -- a Selection/OSLSelection (which Tom mentioned)


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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