extra_fit aligns multiple objects to a reference object.
New in PyMOL 1.7.2
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.
extra_fit [ selection [, reference [, method ]]]
This will align 4 structures on CA atoms using the super method. It will also create an alignment object.
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