Coot and chimera functions

https://github.com/pemsley/coot/blob/master/src/coot.py#L999

To get the transformation matrix:
From COOT SSM:

To transform map in P1
guile command:

fix an atom
Note that COOT is very specific on the atom name: ' C ' (four charactors, first one is space). Chain ID here should not have a space in front.

COOT C++ source for reference:

atom_spec syntax (python)
Note the very specific format for atom names. One leading space, four chars in total (wwPDB specifies cols 13-16, COOT always starts at col 14).

Source: 

Source: 