[chimera-dev] AIMAll extension update 1

[Eric Pettersen]

On Jan 8, 2015, at 10:46 AM, ros <rodrigogalindo at gmail.com> wrote:

> Hello!
> I have been making progress with the extension.  Now you can open the
> mgpviz file and the atoms will be displayed properly with their
> corresponding bonds in #0.1, the nuclear atractors in #0.2 and the
> bond critical bonds in #0.3  It works great!!
> 
> I am adding Helium atoms to represent the critical points:
> 
> atomNACP = mNACP.newAtom(atom1, Element("He")
> 
> and it works fine.
> Is there a way to modify the color and size of each individual atom
> while it is reading the input? Is it possible to modify the default
> properties generated from the connectMolecule() ?  The idea is that it
> displays the original molecule (extracted from the XYZ coordinates) in
> wire representation, and the bond critical points in red (as an
> example) and the other critical points in blue.  Each point group are
> generated in their own separate molecule with different Molecule()
> commands, so, is it possible to modify the visualization properties?

Yes:

a.color = chimera.MaterialColor(red, green, blue, opacity)
a.radius = radius

red / green / blue / opacity all in the range 0-1.

To change to ball and stick, you would set the atoms to balls as you make them:

a.drawMode = chimera.Atom.Ball

and change all the bonds after you've called connectMolecule():

for b in m.bonds:
	b.drawMode = chimera.Bond.Stick

--Eric


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