[Chimera-users] Animate a Reacton Mechanism?

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 21 11:25:45 PST 2012

Hi Kevin,
I imagine you could save positions (savepos command) for the bond-broken and bond-formed structures of the complex and then use the reset command to go from one to the other over a specified number of frames.  You could also save a position at one or more intermediate states, if you wanted to do something at that state (make the "bond" appear or disappear).

The molecules that move relative to one another should be separate models, and since you can't make a bond between separate models, you would need to make a pseudobond.  It could be shown as wire, or dashed line, or stick.  Pseudobonds automatically "stretch" when the endpoints move relative to one another.  You can create it ahead of time (not being a programmer, I would just make a distance monitor and then in Distances tool set its label to "None" and use "display options" button to set initial display style/color), save it in the session, and then with the setattr command control display style, color, and when it appears or disappears.  With [a lot] more work you could gradually fade it in or out by changing the transparency of its color, but there is no single command to do the whole fade, it would take lots of individual color-changing commands.  Example commands to change pseudobond color and and hide pseudobond:

setattr p color 1,0,0,.5
setattr p display 0

... where you could put the atomspec of the two endpoint atoms at the end of each command to control only that pseudobond, instead of all pseudobonds.

With python there may be additional possibilities, such as adding a new atom to one model that is in the same exact place as the real bond partner atom in the other model, then adding an intramodel bond to that new atom, but I think that would be harder anyway, and more limiting, since the bond wouldn't automatically stretch like the pseudobond.  To show it changing length would require changing the internal coordinates of the model. 

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 19, 2012, at 4:09 PM, Kevin D. Walker wrote:

> I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released.
> I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

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