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

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.fitting

tmalign is a python module (or script) that provides wrappers to TMalign, TMscore and MMalign. The executables can be downloaded from and should be saved to any directory in PATH.

The module also provides the command alignwithanymethod which is useful to quickly test different alignment methods (with their respective default values).


All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c speleo3 tmalign


tmalign mobile, target [, args [, exe [, ter [, transform [, object ]]]]]

tmscore and mmalign usage is equivalent.

alignwithanymethod mobile, target [, methods ]


fetch 2xwu 2x19 3gjx, async=0

# TMscore example
tmscore 2x19 and chain B, 2xwu and chain B

# TMalign example with alignment object
tmalign 3gjx and chain A, 2xwu and chain B, object=aln

# full path to executable
mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign

Example for alignwithanymethod (tmalign and cealign will nicely align the beta sheet, but align and super will fail to find a nice superposition):

fetch 1C0M  1BCO, async=0
remove 1C0M and not chain B
alignwithanymethod 1C0M, 1BCO

See Also