Difference between revisions of "Intra fit"
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| − | + | '''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=== | ===USAGE=== | ||
| − | + | <source lang="python"> | |
| − | + | intra_fit (selection),state | |
| + | </source> | ||
| + | |||
===PYMOL API=== | ===PYMOL API=== | ||
| − | + | <source lang="python"> | |
| − | + | cmd.intra_fit( string selection, int state ) | |
| + | </source> | ||
| + | |||
===EXAMPLES=== | ===EXAMPLES=== | ||
| − | + | ==== Simple Selection==== | |
| − | + | <source lang="python"> | |
| + | intra_fit ( name ca ) | ||
| + | </source> | ||
| + | |||
| + | ==== 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: | ||
| + | <source lang="python"> | ||
| + | print cmd.intra_fit(selection, state) | ||
| + | </source> | ||
| + | which will fit all of the other states to the indicated states and return the RMS values as a list. | ||
| + | |||
| + | A simple example is: | ||
| + | <source lang="python"> | ||
| + | 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] | ||
| + | </source> | ||
| + | |||
| + | Note that a RMS value of -1.0 is returned for the target state. | ||
| + | |||
===PYTHON EXAMPLE=== | ===PYTHON EXAMPLE=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | + | from pymol import cmd | |
| − | + | rms = cmd.intra_fit("(name ca)",1) | |
</source> | </source> | ||
===USER EXAMPLES=== | ===USER EXAMPLES=== | ||
| + | ===USER COMMENTS=== | ||
| + | See [[Rms]] for selection caveats for this group of commands. | ||
| + | |||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | + | [[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[Extra_fit]], [[Align]] | |
| − | |||
| − | [[Category:Commands| | + | [[Category:Commands|Intra Fit]] |
| + | [[Category:States|Intra Fit]] | ||
| + | [[Category:Structure_Alignment|Intra Fit]] | ||
Latest revision as of 05:39, 12 June 2017
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 EXAMPLES
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