Extra fit

Type	Python Module
Download	extra_fit.py
Author(s)	Thomas Holder
License	BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

extra_fit aligns multiple objects to a reference object. It can use any of PyMOL's pairwise alignment methods (align, super, cealign, fit...). More precisely it can use any function which takes arguments mobile and target, so it will for example also work with tmalign. Additional keyword arguments are passed to the used method, so you can for example adjust outlier cutoff or create an alignment object.

There are several similar commands/scripts for this job, like "A > align > all to this" from the PyMOL panel, the "alignto" command, align_all.py and super_all.py scripts from Robert Campbell.

Usage

extra_fit [ selection [, reference [, method ]]]

Example

This will align 4 structures on CA atoms using the super method. It will also create an alignment object.

import extra_fit

fetch 1e4y 1ake 4ake 3hpq, async=0
remove not chain A

extra_fit name CA, 1ake, super, object=aln_super

Same, but with tmalign method (see TMalign)

import tmalign
extra_fit name CA, 1ake, tmalign, object=aln_tmalign

See Also

• align_all.py and super_all.py