Super

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

• align
• Cealign