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Difference between revisions of "Intra fit"

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===DESCRIPTION===
+
 
    "intra_fit" fits all states of an object to an atom selection
+
'''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.
  in the specified state.  It returns the rms values to python
+
 
  as an array.
 
 
 
===USAGE===
 
===USAGE===
    intra_fit (selection),state
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<source lang="python">
+
intra_fit (selection),state
 +
</source>
 +
 
 
===PYMOL API===
 
===PYMOL API===
    cmd.intra_fit( string selection, int state )
+
<source lang="python">
+
cmd.intra_fit( string selection, int state )
 +
</source>
 +
 
 
===EXAMPLES===
 
===EXAMPLES===
    intra_fit ( name ca )
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==== 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
+
from pymol import cmd
  rms = cmd.intra_fit("(name ca)",1)
+
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]]
  [[Cmd fit]], [[Cmd rms]], [[Cmd rms_cur]], [[Cmd intra_rms]], [[Cmd intra_rms_cur]], [[Cmd pair_fit]]
 
  
 
   
 
   
[[:Category:Commands| intra_fit]]
+
[[Category:Commands|Intra Fit]]
 +
[[Category:States|Intra Fit]]
 +
[[Category:Structure_Alignment|Intra Fit]]

Latest revision as of 04:31, 26 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