<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 8, 2015, at 10:46 AM, ros <<a href="mailto:rodrigogalindo@gmail.com">rodrigogalindo@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello!<br>I have been making progress with the extension. Now you can open the<br>mgpviz file and the atoms will be displayed properly with their<br>corresponding bonds in #0.1, the nuclear atractors in #0.2 and the<br>bond critical bonds in #0.3 It works great!!<br><br>I am adding Helium atoms to represent the critical points:<br><br>atomNACP = mNACP.newAtom(atom1, Element("He")<br><br>and it works fine.<br>Is there a way to modify the color and size of each individual atom<br>while it is reading the input? Is it possible to modify the default<br>properties generated from the connectMolecule() ? The idea is that it<br>displays the original molecule (extracted from the XYZ coordinates) in<br>wire representation, and the bond critical points in red (as an<br>example) and the other critical points in blue. Each point group are<br>generated in their own separate molecule with different Molecule()<br>commands, so, is it possible to modify the visualization properties?</blockquote><br></div><div>Yes:</div><div><br></div><div>a.color = chimera.MaterialColor(<i>red</i>, <i>green</i>, <i>blue</i>, <i>opacity</i>)</div><div>a.radius = <i>radius</i></div><div><i><br></i></div><div><i>red</i> / <i>green</i> / <i>blue</i> / <i>opacity</i> all in the range 0-1.</div><div><br></div><div>To change to ball and stick, you would set the atoms to balls as you make them:</div><div><br></div><div>a.drawMode = chimera.Atom.Ball</div><div><br></div><div>and change all the bonds after you've called connectMolecule():</div><div><br></div><div>for b in m.bonds:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>b.drawMode = chimera.Bond.Stick</div><div><br></div><div>--Eric</div><div><br></div><br></body></html>