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], a2.coord().data()[dim]))
print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius)
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 Log.

--Eric

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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