On Jan 8, 2015, at 10:46 AM, ros <rodrigogalindo@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