TMalign

Type	Python Module
Download	tmalign.py
Author(s)	Thomas Holder
License	BSD
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.

Usage

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

tmscore and mmalign usage is equivalent.

Examples

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