Intra fit - Revision history

Cchem: 17 revisions

2017-06-26T04:31:23Z

17 revisions

Hongbo zhu at 09:39, 12 June 2017

2017-06-12T09:39:09Z

Hongbo zhu: add extra_fit to reference

2017-06-12T09:38:24Z

add extra_fit to reference

Pyadmin: 1 revision

2014-03-28T02:16:28Z

1 revision

Hongbo zhu: /* USER COMMENTS */

2013-11-20T09:50:28Z

USER COMMENTS

Tlinnet: moved Intra Fit to Intra fit: small letters

2012-01-15T14:28:44Z

moved Intra Fit to Intra fit: small letters

New page

'''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===
<source lang="python">
intra_fit (selection),state
</source>

===PYMOL API===
<source lang="python">
cmd.intra_fit( string selection, int state )
</source>

===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===
<source lang="python">
from pymol import cmd
rms = cmd.intra_fit("(name ca)",1)
</source>

===USER EXAMPLES===

===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[Align]]

[[Category:Commands|Intra Fit]]
[[Category:States|Intra Fit]]
[[Category:Structure_Alignment|Intra Fit]]

Vinnyrose at 14:06, 20 June 2009

2009-06-20T14:06:30Z

New page

===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.

===USAGE===
<source lang="python">
intra_fit (selection),state
</source>

===PYMOL API===
<source lang="python">
cmd.intra_fit( string selection, int state )
</source>

===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===
<source lang="python">
from pymol import cmd
rms = cmd.intra_fit("(name ca)",1)
</source>

===USER EXAMPLES===

===USER COMMENTS===
See [[Intra_Rms]] for selection caveats for this group of commands.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[Align]]

[[Category:Commands|Intra Fit]]
[[Category:States|Intra Fit]]
[[Category:Structure_Alignment|Intra Fit]]

Shiven: /* SEE ALSO */

2006-01-09T18:32:49Z

Tree at 05:23, 21 February 2005

2005-02-21T05:23:44Z

Tree at 05:23, 21 February 2005

2005-02-21T05:23:21Z

← Older revision		Revision as of 09:39, 12 June 2017
Line 52:		Line 52:

	===SEE ALSO===		===SEE ALSO===
−	[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[~~Extra_Fit~~]], [[Align]]	+	[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Rms]], [[Intra_Rms_Cur]], [[Pair_Fit]], [[Extra_fit]], [[Align]]

← Older revision		Revision as of 09:38, 12 June 2017
Line 52:		Line 52:

	===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]]

← Older revision		Revision as of 05:23, 21 February 2005
Line 26:		Line 26:


−	[[Category:Commands ~~intra_fit~~\|intra_fit]]	+	[[Category:Commands\|intra_fit]]

← Older revision		Revision as of 05:23, 21 February 2005
Line 26:		Line 26:


−	[[Category:Commands\| intra_fit]]	+	[[Category:Commands intra_fit\|intra_fit]]

← Older revision	Revision as of 04:31, 26 June 2017
(No difference)

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 49: / Line 49: @@
 ===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===