Super - Revision history

Bell: 1 revision

2015-10-30T15:53:40Z

1 revision

OsvaldoMartin: /* See Also */ add link to Get_raw_alignment

2015-10-28T17:19:47Z

Bell: 1 revision

2014-10-20T15:32:26Z

1 revision

Speleo3 at 21:10, 29 September 2014

2014-09-29T21:10:38Z

Bell: 10 revisions

2014-03-28T03:56:01Z

10 revisions

Tlinnet: /* Write rmsd to file and looping */

2014-01-23T16:44:04Z

Write rmsd to file and looping

Tlinnet: /* Write rmsd to file */

2014-01-23T16:43:35Z

Write rmsd to file

Tlinnet: /* Caveats */

2014-01-23T15:38:29Z

Caveats

New page

'''super''' aligns two selections. '''super''' is more robust and accurate than '''align'''. For syntax, see [[align]].

[[Category:Structure_Alignment|Super]]

=== Algorithm Details ===
'''super''' does a sequence-independent structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance).

== Caveats ==
* If super ever tells you no matched atoms, then instead of
<source lang="python">
super p1, p2
</source>
try
<source lang="python">
super p1 & alt A+'', p2 & alt B+''
</source>

== Write rmsd to file ==

'''pymol_rmsd_test.pml'''
<source lang="python">
reinitialize

fetch 1F9J, async=0
fetch 1YX5, async=0

extract 1F9J_A, 1F9J and chain A
extract 1YX5_B, 1YX5 and chain B

test=cmd.super("1F9J_A","1YX5_B")

python
writefile=open("rmsd_file.txt","a")
writefile.write(' '.join('%s' % x for x in test))
writefile.write('\n')
writefile.close()
python end
</source>

In terminal
<source lang="bash">
pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt
</source>

== See Also ==
* [[align]]
* [[Cealign]]

[[Category:Commands]]

@@ Line 78: / Line 78: @@
 cmd.load("%s.pdb"%prot1)
 cmd.load("%s.pdb"%prot2)
-cmd.load("./ensemblesize2_numstruct100_20140115/%s"%prot3)
+cmd.load("./ensemblesize2_numstruct/%s"%prot3)
 #show_as cartoon, all

← Older revision	Revision as of 15:53, 30 October 2015
(No difference)

@@ Line 112: / Line 112: @@
 * [[align]]
 * [[Cealign]]
 [[Category:Commands]]
 [[Category:Structure_Alignment|Super]]

← Older revision	Revision as of 15:32, 20 October 2014
(No difference)

@@ Line 1: / Line 1: @@
-'''super''' aligns two selections.  '''super''' is more robust and accurate than '''align'''.  For syntax, see [[align]].
+== Usage ==
-[[Category:Structure_Alignment|Super]]
+See [[align]] command.
-=== Algorithm Details ===
+== Caveats ==
-== Caveats ==
+* '''Alternative Conformations:'''  If super ever tells you no matched atoms, then instead of <source lang="python">
 super p1, p2
-</source>
+</source> try <source lang="python">
 super p1 & alt A+'', p2 & alt B+''
 </source>
-== Write rmsd to file ==
+== User Scripts ==
 '''pymol_rmsd_test.pml'''
@@ Line 44: / Line 44: @@
 </source>
-== Write rmsd to file and looping==
+=== Write rmsd to file and looping===
 '''pymol_pymol_loop.sh'''
@@ Line 115: / Line 115: @@
 [[Category:Commands]]

← Older revision	Revision as of 03:56, 28 March 2014
(No difference)

@@ Line 42: / Line 42: @@
 <source lang="bash">
 pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt
 </source>