Editing TMalign

{{Infobox script-repo
|type      = module
|filename  = scripts/tmalign.py
|author    = [[User:Speleo3|Thomas Holder]]
|license   = BSD
}}

{{Infobox psico
|module    =  psico.fitting
}}

'''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 [http://en.wikipedia.org/wiki/PATH_(variable) PATH].

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

== Installation ==

All dependencies are available from [https://anaconda.org Anaconda Cloud]:

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

== Usage ==

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

'''tmscore''' and '''mmalign''' usage is equivalent.

 alignwithanymethod mobile, target [, methods ]

== Examples ==

<syntaxhighlight lang="python">
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
</syntaxhighlight>

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

<syntaxhighlight lang="python">
fetch 1C0M  1BCO, async=0
remove 1C0M and not chain B
alignwithanymethod 1C0M, 1BCO
</syntaxhighlight>

<gallery widths="240" heights="180">
Image:1C0M_align01.png|1C0M_align01
Image:1C0M_super01.png|1C0M_super01
Image:1C0M_cealign01.png|1C0M_cealign01
Image:1C0M_tmalign01.png|1C0M_tmalign01
</gallery>

== See Also ==

* [[align]]
* [[super]]
* [[cealign]]

[[Category:Structure_Alignment]]
[[Category:Script_Library]]
[[Category:Pymol-script-repo]]