TMalign - Revision history

Cchem: 1 revision

2017-11-13T03:27:09Z

1 revision

Speleo3: anaconda

2017-10-19T08:43:09Z

anaconda

Pyadmin: 4 revisions

2014-03-28T01:44:36Z

4 revisions

Tlinnet: /* See Also */

2012-01-15T15:05:03Z

Speleo3: gallery

2011-12-14T10:15:22Z

gallery

Speleo3: alignwithanymethod, see also

2011-12-14T09:49:16Z

alignwithanymethod, see also

Speleo3: new

2011-12-13T19:39:25Z

new

New page

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

'''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].

== Usage ==

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

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

== 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>

[[Category:Structure_Alignment]]
[[Category:Script_Library]]

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	[[Category:Structure_Alignment]]		[[Category:Structure_Alignment]]
	[[Category:Script_Library]]		[[Category:Script_Library]]
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 alignwithanymethod 1C0M, 1BCO
 </syntaxhighlight>
 == See Also ==

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 |author    = [[User:Speleo3|Thomas Holder]]
 |license   = BSD
 }}
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 The module also provides the command '''alignwithanymethod''' which is useful to quickly test different alignment methods (with their respective default values).
 == Usage ==

← Older revision	Revision as of 01:44, 28 March 2014
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 '''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].
 == Usage ==
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 '''tmscore''' and '''mmalign''' usage is equivalent.
 == Examples ==
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 mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign
 </syntaxhighlight>
 [[Category:Structure_Alignment]]
 [[Category:Script_Library]]