[chimera-dev] AIMAll extension update 1

[Eric Pettersen]

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
>> 

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