[Chimera-users] Small molecule dimensions

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 21 11:37:43 PDT 2010

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.



> 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, 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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