This is a read-only mirror of pymolwiki.org

Difference between revisions of "Intra fit"

From PyMOL Wiki
Jump to navigation Jump to search
 
m (17 revisions)
 
(11 intermediate revisions by 4 users not shown)
Line 1: Line 1:
===DESCRIPTION===
+
 
 
'''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.
 
'''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===
intra_fit (selection),state
+
<source lang="python">
 +
intra_fit (selection),state
 +
</source>
  
 
===PYMOL API===
 
===PYMOL API===
Line 11: Line 13:
  
 
===EXAMPLES===
 
===EXAMPLES===
intra_fit ( name ca )
+
==== 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===
Line 22: Line 49:
 
   
 
   
 
===USER COMMENTS===
 
===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.
+
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]], [[Align]]
+
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[Extra_fit]], [[Align]]
  
 
   
 
   
[[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