[Chimera-users] Massive superposing...

Yasser Almeida Hernández pedro.al at fenhi.uh.cu
Thu Jan 21 15:15:43 PST 2010

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  

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...

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

Correo FENHI

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