[chimera-dev] AIMAll extension update 1

[ros]

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?

Thank you!

Rodrigo.



On Wed, Jan 7, 2015 at 2:01 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Rodrigo,
> I covered this in my initial, novella-length response:
>
> Fake Atoms
> In this scenario, you would create a second Molecule as you read the file
> and add the critical points as atoms to that.  You include the additional
> Molecule in the list of models you return ("return [m, m2]").   You would
> not call connectMolecule() on the second Molecule, but might add pseudobonds
> from the critical points to the appropriate atoms (you can't add regular
> bonds between models).  The second molecule will have the same ID and sub-ID
> # as the first one, and will move in tandem with it.  It will show up in the
> model panel.
>
> There really is no such thing as a fake Molecule per se.  You just use the
> Molecule class in exactly the same way as for a normal molecule.  It's just
> that what you're trying to depict isn't an actual chemical entity.  One
> thing I probably should have added, is that for the "fake" Molecule that
> will hold the critical points you should set the attribute "isRealMolecule"
> to False, like so:
>
> m2.isRealMolecule = False
>
> This will prevent the critical-points Molecule from being listed in various
> interfaces that really only want to list actual chemical entities (e.g. the
> Minimize interface).
>
> --Eric
>
> On Jan 7, 2015, at 11:59 AM, ros <rodrigogalindo at gmail.com> wrote:
>
> That did the trick, the bonds are now correctly being displayed! Thank you!
>
> Could you please provide an example for drawing or placing a fake
> atom? I do not seem to find the correct command in the Programmers
> manual.
>
> Thank you again,
>
> Rodrigo.
>
> On Wed, Jan 7, 2015 at 12:50 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> On Jan 7, 2015, at 11:45 AM, Eric Pettersen <pett at cgl.ucsf.EDU> wrote:
>
> So I guess the question is:  what is up with the AIMAll coordinates?
>
>
> I see.  AIMAll units are bohrs.  So you need to multiply by 0.52918.
>
> --Eric
>
>