Difference between revisions of "TMalign"

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|author    = [[User:Speleo3|Thomas Holder]]
 
|author    = [[User:Speleo3|Thomas Holder]]
 
|license  = BSD
 
|license  = BSD
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}}
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{{Infobox psico
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|module    =  psico.fitting
 
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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].
 
'''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].
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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).
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== Installation ==
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All dependencies are available from [https://anaconda.org Anaconda Cloud]:
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conda install -c schrodinger pymol
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conda install -c schrodinger pymol-psico
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conda install -c speleo3 tmalign
  
 
== Usage ==
 
== Usage ==
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'''tmscore''' and '''mmalign''' usage is equivalent.
 
'''tmscore''' and '''mmalign''' usage is equivalent.
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alignwithanymethod mobile, target [, methods ]
  
 
== Examples ==
 
== Examples ==
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mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign
 
mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign
 
</syntaxhighlight>
 
</syntaxhighlight>
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Example for '''alignwithanymethod''' (tmalign and [[cealign]] will nicely align the beta sheet, but [[align]] and [[super]] will fail to find a nice superposition):
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<syntaxhighlight lang="python">
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fetch 1C0M  1BCO, async=0
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remove 1C0M and not chain B
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alignwithanymethod 1C0M, 1BCO
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</syntaxhighlight>
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<gallery widths="240" heights="180">
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Image:1C0M_align01.png|1C0M_align01
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Image:1C0M_super01.png|1C0M_super01
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Image:1C0M_cealign01.png|1C0M_cealign01
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Image:1C0M_tmalign01.png|1C0M_tmalign01
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</gallery>
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== See Also ==
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* [[align]]
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* [[super]]
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* [[cealign]]
  
 
[[Category:Structure_Alignment]]
 
[[Category:Structure_Alignment]]
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
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[[Category:Pymol-script-repo]]

Latest revision as of 04:43, 19 October 2017

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

Included in psico
This command or function is available from psico, which is a PyMOL extension.

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 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 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

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

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

fetch 1C0M  1BCO, async=0
remove 1C0M and not chain B
alignwithanymethod 1C0M, 1BCO

See Also