[Chimera-users] Small molecule dimensions

le monk le_monk at hotmail.com
Wed Apr 21 11:20:01 PDT 2010

Thank you Eric - this is really helpful. But as these are minimum x y z 
lengths then the reported dimensions will be different if the molecules 
coordinates were transformed. Can this script be modified to give the 
minimum dimensions of the molecule (not just the x y z dimensions)? For 
example, can a box be drawn around the Van der Waal radii whose volume 
was the minimum possible for that molecule, and report the lengths of each
 of its dimensions? This would be really nice to directly compare the 
size of small molecules.

Many thanks 

CC: chimera-users at cgl.ucsf.edu
From: pett at cgl.ucsf.edu
To: le_monk at hotmail.com
Subject: Re: [Chimera-users] Small molecule dimensions
Date: Sun, 18 Apr 2010 07:52:31 -0700

Yes, something like this:
from chimera import openModels, Moleculefor 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 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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