[Chimera-users] Small molecule dimensions
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.
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.coord().data()[dim] - atoms.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?
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