|This code has been put under version control in the project Pymol-script-repo|
tmalign is a python module (or script) that provides wrappers to TMalign, TMscore and MMalign. The executables can be downloaded from http://zhanglab.ccmb.med.umich.edu/TM-align/ 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).
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
fetch 1C0M 1BCO, async=0 remove 1C0M and not chain B alignwithanymethod 1C0M, 1BCO