[Chimera-users] Bonds vs. Pseudobonds

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 24 12:20:15 PDT 2009

Hi Thomas,
	I would recommend against adding regular covalent bonds between the  
metal and its coordinating atoms since Chimera's atom-typing code  
isn't designed to handle coordination covalent bonds, so any chemistry- 
related computations (hydrogen addition, charge assignment, etc.)  
involving the complex would be wacky afterward.  I would instead  
recommend you just get the pseudobonds depicted however you prefer.   
You can do this by control-clicking one of the pseudobonds to select  
it, then hit up arrow to select all the pseudobonds in all complexes  
in the molecule, then bring up the Selection Inspector (by clicking  
the green button at the lower right of the Chimera window).  In that  
you can change the color of the pseudobonds, whether then are depicted  
as wire or stick, etc.  If you change to the "Pseudobond Group" item  
of the dialog's "Inspect" menu, you can change the line dashing of the  
pseudobonds.  The group also has a color, which is used for any  
pseudobond whose individual color is "No color".
	There is also limited control as to how metal complexes look in new  
models in the "New Molecules" preference category (Favorites- 
	If you must create regular bonds to the metal for some reason there  
are two methods.  You can control double-click a pseudobond and choose  
"Select Bonded" from the popup menu, then type "bond sel" in the  
command line -- or you can bring up the Pseudobond Panel with General  
Controls->Pseudobond Panel and choose the coordination complexes and  
hit the "select bonded" button, then use Structure Editing->Build  
Structure, choose the Add/Delete Bonds tab and click the Add button  
(with the menu set to "reasonable bonds").


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Mar 24, 2009, at 9:31 AM, Dipl.-Ing. Thomas Mitterfellner wrote:

> Hello again!
> I have a structure containing Germanium bonded to three oxygens and  
> one
> methyl group. By default, all of the bonds between Germanium and its
> valences are considered as pseudobonds and hence drawn as such.
> In the manual, I read that Chimera uses an algorithm that considers
> atoms classically bonded if the distance is below the sum of their VDW
> radii (plus a margin of 0.4 A). However, no matter what I set the  
> radius
> of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to
> display a regular bond between Ge and its valences.
> Can you give me a hint how to set a rule when a normal bond is  
> drawn, or
> how I can draw one manually?
> Thank you very much,
> Thomas
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