Intra fit

intra_fit fits all states of an object to an atom selection in the specified state. It returns the rms values to python as an array.

USAGE

intra_fit (selection),state

PYMOL API

cmd.intra_fit( string selection, int state )

EXAMPLES

Simple Selection

intra_fit ( name ca )

Fitting NMR Ensembles

Warren provided a great example on the PyMOL list. If the NMR ensemble has all the structures loaded as multiple states (which is the default behavoir (see split_states) for multimodel PDBs) then we can simply call:

print cmd.intra_fit(selection, state)

which will fit all of the other states to the indicated states and return the RMS values as a list.

A simple example is:

fetch 1i8e, async=0
print cmd.intra_fit("1i8e////CA", 1)

# results:
[-1.0, 1.1934459209442139, 1.2950557470321655, 0.71329855918884277,
0.76704370975494385, 0.78973227739334106, 0.99323123693466187,
1.0165935754776001, 0.6535714864730835, 0.95591926574707031,
1.1299723386764526, 0.28637325763702393, 0.69836461544036865,
0.40816938877105713, 1.1637680530548096]

Note that a RMS value of -1.0 is returned for the target state.

PYTHON EXAMPLE

from pymol import cmd
rms = cmd.intra_fit("(name ca)",1)

USER COMMENTS

See Rms for selection caveats for this group of commands.

SEE ALSO

Fit, Rms, Rms_Cur, Intra_Rms, Intra_Rms_Cur, Pair_Fit, Extra_Fit, Align