Super

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super aligns two selections. super is more robust and accurate than align. For syntax, see align.

Contents

Algorithm Details

super does a sequence-independent structure-based dynamic programming 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).

Caveats

super p1, p2

try

super p1 & alt A+'', p2 & alt B+''

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

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