Align: Difference between revisions
(Added a very helpful tip provided by Warren.) |
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int skip=0, string object=None, string matrix="BLOSUM62", | int skip=0, string object=None, string matrix="BLOSUM62", | ||
int quiet=1 ) | int quiet=1 ) | ||
</source> | |||
===EXAMPLES=== | |||
<source lang="python"> | |||
align prot1////CA, prot2, object=alignment | |||
</source> | </source> | ||
===NOTE=== | ===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 | ||
- 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"> | <source lang="python"> | ||
align | set all_states, on | ||
intra_fit <your_structure_1> | |||
intra_fit <your_structure_2> | |||
align <your_structure_1>////CA, <your_structure_2>////CA | |||
</source> | </source> | ||
===SEE ALSO=== | ===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]] [[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]] | ||
[[Category:Commands|align]] | [[Category:Commands|align]] | ||
Revision as of 13:30, 9 January 2006
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.
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
- 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
SEE ALSO
fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit, intra_fit, Kabsch