[Chimera-users] Small molecule dimensions

Eric Pettersen pett at cgl.ucsf.edu
Sun Apr 18 07:52:31 PDT 2010

Yes, something like this:

from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	print m.name
	atoms = m.atoms
	for dim in range(3):
		atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim],  
		print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] -  
		print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim]  
- atoms[-1].radius)

Put the above in a file ending in ".py" and open it in Chimera and it  
will print the min/max xyz values accounting for radius in the Reply  


	Eric Pettersen
	UCSF Computer Graphics Lab

On Apr 16, 2010, at 10:46 AM, le monk wrote:

> Hello,
> I have a few pdb files of small molecules that I would like to know  
> the dimensions of. Is it possible to use Chimera the measure the  
> minimum x y z lengths - taking into account Van der Waals radii? Or  
> perhaps you could suggest other software for this?
> Many thanks
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