Difference between revisions of "Super"

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=== Overview ===
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'''super''' aligns two selections.
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'''super''' aligns two selections. '''super''' is more robust and accurate than '''align'''.  For syntax, see [[align]].
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It does a '''sequence-independent''' (unlike [[align]]) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (just like [[align]]).
 +
'''super''' is more robust than '''align''' for proteins with low sequence similarity.
  
 +
== Usage ==
 +
 +
See [[align]] command.
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 +
== Caveats ==
 +
 +
* '''Alternative Conformations:'''  If super ever tells you no matched atoms, then instead of <source lang="python">
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super p1, p2
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</source> try <source lang="python">
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super p1 & alt A+'', p2 & alt B+''
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</source>
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 +
== User Scripts ==
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=== Write rmsd to file ===
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'''pymol_rmsd_test.pml'''
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<source lang="python">
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reinitialize
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 +
fetch 1F9J, async=0
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fetch 1YX5, async=0
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extract 1F9J_A, 1F9J and chain A
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extract 1YX5_B, 1YX5 and chain B
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 +
test=cmd.super("1F9J_A","1YX5_B")
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python
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writefile=open("rmsd_file.txt","a")
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writefile.write(' '.join('%s' % x for x in test))
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writefile.write('\n')
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writefile.close()
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python end
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</source>
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In terminal
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<source lang="bash">
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pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt
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</source>
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=== Write rmsd to file and looping===
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'''pymol_pymol_loop.sh'''
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<source lang="bash">
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#!/bin/csh -f
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set x = 1
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while ( $x <= 20 )
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set prot="energy_${x}.pdb"
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pymol -c pymol_super.pml $prot
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@ x = $x + 1
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end
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</source>
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'''pymol_super.pml'''
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<source lang="python">
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reinitialize
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import sys
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python
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prot1="XXXX"
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prot2="YYYY_trimmed"
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prot3=sys.argv[3]
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#prot3="energy_54.pdb"
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prot3name=prot3.split(".pdb")[0]
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print prot3, prot3name
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python end
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cd /XXXXX
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cmd.load("%s.pdb"%prot1)
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cmd.load("%s.pdb"%prot2)
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cmd.load("./ensemblesize2_numstruct/%s"%prot3)
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#show_as cartoon, all
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align1=cmd.super("%s"%prot3name,"%s"%prot1)
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print align1
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python
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writefile=open("pymol_rmsd_file.txt","a")
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writefile.write('%s %s '%(prot3name, prot1))
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writefile.write(' '.join('%s' % x for x in align1))
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writefile.write(' ')
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python end
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align2=cmd.super("%s"%prot3name,"%s"%prot2)
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print align2
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python
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writefile=open("pymol_rmsd_file.txt","a")
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writefile.write('%s %s '%(prot3name, prot2))
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writefile.write(' '.join('%s' % x for x in align2))
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writefile.write('\n')
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writefile.close()
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python end
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</source>
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In terminal
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<source lang="bash">
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chmod +x pymol_loop.sh
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./pymol_loop.sh
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</source>
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== See Also ==
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* [[align]]
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* [[Cealign]]
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* [[Get_raw_alignment]]
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[[Category:Commands]]
 
[[Category:Structure_Alignment|Super]]
 
[[Category:Structure_Alignment|Super]]
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=== Algorithm Details ====
 
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'''super''' does a BLAST-like BLOSUM62-weighted dynamic programming sequence alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance).  Next, it does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy.
 

Latest revision as of 13:19, 28 October 2015

super aligns two selections. It does a sequence-independent (unlike align) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (just like align). super is more robust than align for proteins with low sequence similarity.

Usage

See align command.

Caveats

  • Alternative Conformations: If super ever tells you no matched atoms, then instead of 
    super p1, p2
    try 
    super p1 & alt A+'', p2 & alt B+''

User Scripts

Write rmsd to file

pymol_rmsd_test.pml 

reinitialize

fetch 1F9J, async=0
fetch 1YX5, async=0

extract 1F9J_A, 1F9J and chain A
extract 1YX5_B, 1YX5 and chain B

test=cmd.super("1F9J_A","1YX5_B")

python
writefile=open("rmsd_file.txt","a")
writefile.write(' '.join('%s' % x for x in test))
writefile.write('\n')
writefile.close()
python end

In terminal 

pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt

Write rmsd to file and looping

pymol_pymol_loop.sh 

#!/bin/csh -f
set x = 1

while ( $x <= 20 )
	set prot="energy_${x}.pdb"
	pymol -c pymol_super.pml $prot
	@ x = $x + 1
end


pymol_super.pml 

reinitialize
import sys

python 
prot1="XXXX"
prot2="YYYY_trimmed"

prot3=sys.argv[3]
#prot3="energy_54.pdb"
prot3name=prot3.split(".pdb")[0]
print prot3, prot3name
python end

cd /XXXXX

cmd.load("%s.pdb"%prot1)
cmd.load("%s.pdb"%prot2)
cmd.load("./ensemblesize2_numstruct/%s"%prot3)
#show_as cartoon, all

align1=cmd.super("%s"%prot3name,"%s"%prot1)
print align1

python
writefile=open("pymol_rmsd_file.txt","a")
writefile.write('%s %s '%(prot3name, prot1))
writefile.write(' '.join('%s' % x for x in align1))
writefile.write(' ')
python end

align2=cmd.super("%s"%prot3name,"%s"%prot2)
print align2

python
writefile=open("pymol_rmsd_file.txt","a")
writefile.write('%s %s '%(prot3name, prot2))
writefile.write(' '.join('%s' % x for x in align2))
writefile.write('\n')
writefile.close()
python end

In terminal 

chmod +x pymol_loop.sh
./pymol_loop.sh

See Also

Retrieved from "http://pymolwiki.org/index.php?title=Super&oldid=12180"