Super

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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.

Contents

Usage

See align command.

Caveats

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

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