On Apr 21, 2010, at 11:20 AM, le monk wrote:

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.

The function used in the script (coord()) uses untransformed coordinates.  xformcoord() would use transformed coordinates.

Can this script be modified to give the minimum dimensions of the molecule (not just the x y z dimensions)?

What would be the algorithm for computing that?

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?

Again, how?

You can get a rough estimate by using the Axes tool to draw an axis along the principal axis of the molecule, with the axis radius equal to the average atom-atom distance from the axis.  The axes information can be saved to a file.

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes

--Eric

This would be really nice to directly compare the size of small molecules.

Many thanks 

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CC: chimera-users@cgl.ucsf.edu
From: pett@cgl.ucsf.edu
To: le_monk@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, 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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