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Did you know...
 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.
Usage
align mobile, target [, cutoff [, cycles
[, gap [, extend [, max_gap [, object
[, matrix [, mobile_state [, target_state
[, quiet [, max_skip [, transform [, reset ]]]]]]]]]]]]]
Arguments
- mobile = string: atom selection of mobile object
- target = string: atom selection of target object
- cutoff = float: outlier rejection cutoff in RMS {default: 2.0}
- cycles = int: maximum number of outlier rejection cycles {default: 5}
- gap, extend, max_gap: sequence alignment parameters
- object = ..→
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 A Random PyMOL-generated Cover. See Covers.
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