|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.
tmalign mobile, target [, args [, exe [, ter [, transform [, object ]]]]]
tmscore and mmalign usage is equivalent.
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