Align

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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.

Contents

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).

Your can write the final alignment to a file see save.

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 mobile, string target, float cutoff=2.0,
           int cycles=5, float gap=-10.0, float extend=-0.5,
           int max_gap=50, string object=None, string matrix='BLOSUM62',
           int mobile_state=0, int target_state=0, int quiet=1,
           int max_skip=0, int transform=1, int reset=0 )

This returns a list with 7 items:

  1. RMSD after refinement
  2. Number of aligned atoms after refinement
  3. Number of refinement cycles
  4. RMSD before refinement
  5. Number of aligned atoms before refinement
  6. Raw alignment score
  7. Number of residues aligned

EXAMPLES

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

NOTE

ExecutiveAlign: invalid selections for alignment.

You can skirt this problem by making a temporary object and aligning your original to the copy.

 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

Fitting

fit, pair_fit, intra_fit, Extra_fit
Kabsch, Cealign, tmalign, super
Color_by_conservation, align_all.py and super_all.py.

RMS values

rms, rms_cur, intra_rms, intra_rms_cur

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