This is a read-only mirror of pymolwiki.org
Difference between revisions of "TMalign"
(new) |
m (1 revision) |
||
| (5 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 | ||
}} | }} | ||
'''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]. | ||
| + | |||
| + | 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 13: | Line 27: | ||
'''tmscore''' and '''mmalign''' usage is equivalent. | '''tmscore''' and '''mmalign''' usage is equivalent. | ||
| + | |||
| + | alignwithanymethod mobile, target [, methods ] | ||
== Examples == | == Examples == | ||
| Line 28: | Line 44: | ||
mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign | mmalign 3gjx, 2x19, exe=/usr/local/src/TM/MMalign | ||
</syntaxhighlight> | </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: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 | |
| 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
1C0M_align01
1C0M_super01
1C0M_cealign01
1C0M_tmalign01
