[chimera-dev] Coordination bonds treated as covalent

[Eric Pettersen]

On Jul 19, 2013, at 5:54 AM, Jean Didier Pie Marechal <JeanDidier.Marechal at uab.cat> wrote:

> Hi guys,
> 
> I am  preparing a movie in which I want an organometallic compound linked to an organic one to rotate around the bound between both moieties. Do to so, I need the whole first coordination sphere of the metal and the metal itself to behave as a unique block. If I generate bonds with chimera (covalent) I can do that. Unfortunately, if I keep the session and open back, the bonds have been changed by pseudo bonds (which is actually A LOT BETTER!) but pseudo bonds does not allow the first coordination sphere to behave as a block. I wonder what is the best to solve this problem? Can atoms related by pseudobonds be set (even from the python shell) to be rigid?

Hi JD,
	No, there is no way to have pseudobonds be "rigid", pretty much by definition.  Nonetheless, if you have added covalent bonds between the metal and its coordinating atoms, then saving a session should preserve that change.  Restoring a session is supposed to bring back the exact state you saved, not change it even if the change is an "improvement".  So send me the session that isn't restoring those covalent bonds and I will investigate why they're being changed back into pseudobonds when they shouldn't be.

--Eric


                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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