This is a read-only mirror of pymolwiki.org

Difference between revisions of "TMalign"

From PyMOL Wiki
Jump to navigation Jump to search
(alignwithanymethod, see also)
m (1 revision)
 
(4 intermediate revisions by 3 users not shown)
Line 4: Line 4:
 
|author    = [[User:Speleo3|Thomas Holder]]
 
|author    = [[User:Speleo3|Thomas Holder]]
 
|license  = BSD
 
|license  = BSD
 +
}}
 +
 +
{{Infobox psico
 +
|module    =  psico.fitting
 
}}
 
}}
  
Line 9: Line 13:
  
 
The module also provides the command '''alignwithanymethod''' which is useful to quickly test different alignment methods (with their respective default values).
 
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 ==
 
== Usage ==
Line 40: Line 52:
 
alignwithanymethod 1C0M, 1BCO
 
alignwithanymethod 1C0M, 1BCO
 
</syntaxhighlight>
 
</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 ==
 
== See Also ==
Line 49: Line 68:
 
[[Category:Structure_Alignment]]
 
[[Category:Structure_Alignment]]
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
 +
[[Category:Pymol-script-repo]]

Latest revision as of 03:27, 13 November 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