Difference between revisions of "Align"

Revision as of 15:24, 19 March 2009

DESCRIPTION

align performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit. For comparing proteins with lower sequence identity, an alignment program like, Cealign might be a better choice.

Algorithm Details

align does a BLAST-like BLOSUM62-weighted dynamic programming sequence 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).

Super!

PyMOL now has another command -- super. Super allows for much more robust alignments. It's fast, and under testing, does MUCH better than the original align command.

USAGE

align (source), (target) [,cutoff [,cycles [,gap [,extend \
      [,skip [,object [,matrix [, quiet ]]]]]]]]

PYMOL API

cmd.align( string source, string target, float cutoff=2.0,
           int cycles=2, float gap=-10.0, float extend=-0.5,
           int skip=0, string object=None, string matrix="BLOSUM62",
           int quiet=1 )

EXAMPLES

align  prot1////CA, prot2, object=alignment

NOTE

If object is not None, then align will create an object which indicates which atoms were paired between the two structures

Important note: the molecules you want to align need to be in two different objects. Else, PyMol will answer with a rather cryptic error:

ExecutiveAlign: invalid selections for alignment.

Sometimes Align may appear to give a mediocre fit. This is not due to any shortcoming of the algorithm or Pymol for that matter. This usually happens if one or more of the objects, that you are trying to align, have multiple states. For instance, certain PDB files may contain multiple structures/ensembles of the same protein. This is especially true for PDB files containing NMR structures. The workaround in such a situation is to use this workflow (provided by Warren - thanks!):

 set all_states, on
 intra_fit <your_structure_1>
 intra_fit <your_structure_2>
 align <your_structure_1>////CA, <your_structure_2>////CA

@@ Line 1: / Line 1: @@
 ===DESCRIPTION===
-'''align''' performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit.
+'''align''' performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit.  For comparing proteins with lower sequence identity, an alignment program like, [[Cealign]] might be a better choice.
+==== Algorithm Details ====
+'''align''' does a BLAST-like BLOSUM62-weighted dynamic programming sequence 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).
+=== Super! ===
+PyMOL now has another command -- '''[[super]]'''.  Super allows for much more robust alignments.  It's fast, and under testing, does MUCH better than the original '''align''' command.
 ===USAGE===
@@ Line 22: / Line 28: @@
 ===NOTE===
-- If object is not None, then align will create an object which indicates which atoms were paired between the two structures
+* If object is not None, then align will create an object which indicates which atoms were paired between the two structures
+* <b>Important note: </b> the molecules you want to align need to be in two different objects. Else, PyMol will answer with a rather cryptic error:
+<source lang="python">
+ExecutiveAlign: invalid selections for alignment.
+</source>
-- Sometimes Align may appear to give a mediocre fit. This is not due to any shortcoming of the algorithm or Pymol for that matter. This usually happens if one or more of the objects, that you are trying to align, have multiple states. For instance, certain PDB files may contain multiple structures/ensembles of the same protein. This is especially true for PDB files containing NMR structures. The workaround in such a situation is to use this workflow (provided by Warren - thanks!):
+* Sometimes Align may appear to give a mediocre fit. This is not due to any shortcoming of the algorithm or Pymol for that matter. This usually happens if one or more of the objects, that you are trying to align, have multiple states. For instance, certain PDB files may contain multiple structures/ensembles of the same protein. This is especially true for PDB files containing NMR structures. The workaround in such a situation is to use this workflow (provided by Warren - thanks!):
 <source lang="python">
   set all_states, on
@@ Line 33: / Line 45: @@
 ===SEE ALSO===
-[[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]], [[Cmd intra_fit|intra_fit]], [[Kabsch]]
+[[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]], [[Cmd intra_fit|intra_fit]], [[Kabsch]], [[Cealign]].
 [[Category:Commands|align]]
+[[Category:Structure_Alignment|align]]

Difference between revisions of "Align"

Revision as of 15:24, 19 March 2009

Contents