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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. | ||
| − | + | == Usage == | |
| − | [[ | + | See [[align]] command. |
| − | === | + | == Caveats == |
| − | |||
| − | + | * '''Alternative Conformations:''' If super ever tells you no matched atoms, then instead of <source lang="python"> | |
| − | * If super ever tells you no matched atoms, then instead of | ||
| − | <source lang="python"> | ||
super p1, p2 | super p1, p2 | ||
| − | </source> | + | </source> try <source lang="python"> |
| − | try | ||
| − | <source lang="python"> | ||
super p1 & alt A+'', p2 & alt B+'' | super p1 & alt A+'', p2 & alt B+'' | ||
</source> | </source> | ||
| − | == Write rmsd to file == | + | == User Scripts == |
| + | |||
| + | === Write rmsd to file === | ||
'''pymol_rmsd_test.pml''' | '''pymol_rmsd_test.pml''' | ||
| Line 42: | Line 42: | ||
<source lang="bash"> | <source lang="bash"> | ||
pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt | pymol -c pymol_rmsd_test.pml ; tail -n 1 rmsd_file.txt | ||
| + | </source> | ||
| + | |||
| + | === Write rmsd to file and looping=== | ||
| + | |||
| + | '''pymol_pymol_loop.sh''' | ||
| + | <source lang="bash"> | ||
| + | #!/bin/csh -f | ||
| + | set x = 1 | ||
| + | |||
| + | while ( $x <= 20 ) | ||
| + | set prot="energy_${x}.pdb" | ||
| + | pymol -c pymol_super.pml $prot | ||
| + | @ x = $x + 1 | ||
| + | end | ||
| + | </source> | ||
| + | |||
| + | |||
| + | '''pymol_super.pml''' | ||
| + | <source lang="python"> | ||
| + | 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 | ||
| + | </source> | ||
| + | |||
| + | In terminal | ||
| + | <source lang="bash"> | ||
| + | chmod +x pymol_loop.sh | ||
| + | ./pymol_loop.sh | ||
</source> | </source> | ||
| Line 47: | Line 112: | ||
* [[align]] | * [[align]] | ||
* [[Cealign]] | * [[Cealign]] | ||
| + | * [[Get_raw_alignment]] | ||
[[Category:Commands]] | [[Category:Commands]] | ||
| + | [[Category:Structure_Alignment|Super]] | ||
Latest revision as of 15:53, 30 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 try
super p1, p2
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