[Chimera-users] Massive superposing...

[Yasser Almeida Hernández]

Hi...
I'm performing a massive superposing of aminoacids in different  
conformations. The first model is a arginine "template" reference  
structure that is the fixed model in all matching iterations. I've  
loaded 236 models and i want to match the arginine guanidine group on  
the template guanidine. In each iteration i execute two matching, with  
different atoms selections. The first selection is the "right"  
selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection:  
CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show  
that with the minimal RMSD between the guanidine groups. This is the  
code:

import chimera
from chimera import runCommand

right = "@CD,NE,CZ,NH1,NH2"
inverse = "@CD,NE,CZ,NH2,NH1"

for i in range(2,328):
	print "Superposing..."
	runCommand("match #"+str(i)+right+" #0"+right+"; close 1")
	right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1")

         runCommand("match #"+str(i)+right+" #0"+right+"; close 1")
	inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1")

	if right < inverse:
		print "Minimum RMSD =",right,"\n\n"
		runCommand("match #"+str(i)+right+" #0"+right+"; close 1")

	elif right > inverse:
		print "Minimum RMSD =",inverse_rmsd,"\n\n"
		runCommand("match #"+str(i)+right+" #0"+right+"; close 1")

In principle this script should show the matching with the minimum  
RMSD, but it doesn't work.

Please, help...
Thanks

-- 
Yasser Almeida Hernández, BSc
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 246

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