Align

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Two proteins after structure alignment

align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit. align does a good job on proteins with decent sequence similarity (identity >30%). For comparing proteins with lower sequence identity, the super and cealign commands perform better.

Contents

Usage

align mobile, target [, cutoff [, cycles
    [, gap [, extend [, max_gap [, object
    [, matrix [, mobile_state [, target_state
    [, quiet [, max_skip [, transform [, reset ]]]]]]]]]]]]]

Arguments

Alignment Objects

An alignment object can be created with the object=somename argument. An alignment object provides:

RMSD

The RMSD of the aligned atoms (after outlier rejection!) is reported in the text output. The all-atom RMSD can be obtained by setting cycles=0 and thus not doing any outlier rejection. The RMSD can also be captured with a python script, see the API paragraph below.

Examples

fetch 1oky 1t46, async=0
 
# 1) default with outlier rejection
align 1oky, 1t46
 
# 2) with alignment object, save to clustalw file
align 1oky, 1t46, object=alnobj
save alignment.aln, alnobj
 
# 3) all-atom RMSD (no outlier rejection) and without superposition
align 1oky, 1t46, cycles=0, transform=0

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

Notes

See Also

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