Intra rms - Revision history

Pyadmin: 17 revisions

2014-03-28T01:47:10Z

17 revisions

Hongbo zhu: user comments had been removed for its irrelevance. They are copied to rms page given its importance and add a link to the page.

2013-11-20T09:52:00Z

user comments had been removed for its irrelevance. They are copied to rms page given its importance and add a link to the page.

Tlinnet: moved Intra Rms to Intra rms: small letters

2012-01-15T14:30:29Z

moved Intra Rms to Intra rms: small letters

Speleo3: remove example (it did not work properly and was actually not an intra_rms example...)

2012-01-05T22:42:26Z

remove example (it did not work properly and was actually not an intra_rms example...)

New page

'''intra_rms''' calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

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

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

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]

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

Vinnyrose at 14:06, 20 June 2009

2009-06-20T14:06:47Z

New page

===DESCRIPTION===
'''intra_rms''' calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

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

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

===USER EXAMPLES/COMMENTS===
[[Fit]], [[Rms]], [[Rms_Cur]] are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.

PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,
rms_cur A, D
won't work, due to the aforementioned reason. To fix this, one needs to do,
alter all,segi=""
alter all,chain=""
alter D, resi=str(int(resi)+1) # I don't actually use this line
and now
rms_cur A, D
should work.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]

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

Asceyman: /* USER EXAMPLES/COMMENTS */

2007-09-18T11:52:45Z

USER EXAMPLES/COMMENTS

New page

Tree: /* USER EXAMPLES/COMMENTS */

2005-05-23T14:52:13Z

USER EXAMPLES/COMMENTS

New page

===DESCRIPTION===
"intra_rms" calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

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

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

===USER EXAMPLES/COMMENTS===
[[Fit]], [[Rms]], [[Rms_Cur]] are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.

PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,
rms_cur A, D
won't work, due to the aforementioned reason. To fix this, one needs to do,
alter all,segi=''
alter all,chain=''
alter D, resi=str(int(resi)+1) # I don't actually use this line
and now
rms_cur A, D
should work.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]

[[Category:Commands|intra_rms]]

Tree: /* SEE ALSO */

2005-02-21T05:30:14Z

Tree at 05:27, 21 February 2005

2005-02-21T05:27:00Z

Tree: /* SEE ALSO */

2005-02-21T05:26:47Z

@@ Line 18: / Line 18: @@
 ===SEE ALSO===
-    fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit
+    [[Cmd fit]], [[Cmd rms]], [[Cmd rms_cur]], [[Cmd intra_fit]], [[Cmd intra_rms_cur]], [[Cmd pair_fit ]]
 [[Category:Commands|intra_rms]]

← Older revision		Revision as of 05:27, 21 February 2005
Line 20:		Line 20:
	fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit		fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit

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

← Older revision		Revision as of 05:26, 21 February 2005
Line 20:		Line 20:
	fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit		fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit

−	[[:Category:Commands\|intra_rms]]~~</source>~~	+	[[:Category:Commands\|intra_rms]]

← Older revision	Revision as of 01:47, 28 March 2014
(No difference)

@@ Line 11: / Line 11: @@
 rms = cmd.intra_rms("(name ca)",1)
 </source>
 ===SEE ALSO===

← Older revision	Revision as of 14:30, 15 January 2012
(No difference)