[Chimera-users] Small molecule dimensions
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?
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
> 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],
> 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:
> 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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