[Chimera-users] MatchMaker working beautifully, and Transform Coordinates definitely does move things....

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 17 08:43:32 PST 2017

> On Feb 17, 2017, at 3:47 AM, Steven D. Aird <steven.d.aird at gmail.com> wrote:
> Dear Elaine,
> I apologize for the deluge of Email, but within minutes of writing you, I figured out how to use MatchMaker to align two ribbon models of interest.  Again, it’s simple and elegant.
> I also found the transform coordinates command, which I had missed earlier.  That enables me to move one of the models relative to the other.  But moving a model is tricky because it seems impossible to know what relationship the two models have with a Cartesian coordinate system. I had assumed that x, y, and z would be relative to the monitor surface, but that is not the case.
> Is there a more intuitive way to move molecules while maintaining the same relative orientation?
> Thanks very much for your help.
> Sincerely yours,
> Steve

Hi Steve,
Thanks for the kind words!

After you use Matchmaker (or matrixcopy or the mouse or some other method) to position structures relative to one another, you shouldn’t have to do anything special… now when you move “everything” they will still retain their relationships.  I.e. you can rotate and translate everything with the mouse and structures will still be superimposed, docked, etc. as they were after you moved them separately.

Personally I never use the  Transform Coordinates tool and I don’t understand why you wanted to use it.  You can translate and rotate relative to screen coordinates (X horizontal Y vertical Z normal to screen) using commands “move” and “turn”  and these can apply to everything or only certain models (they have a “models” keyword option).  You can also move only certain models with the mouse by activating/deactivating (freezing) them with the “A” checkboxes in the Model Panel, which can be opened from the Favorites menu.

Also, for future reference, we really prefer questions to be sent to chimera-users (CC’d here) so that other people can benefit from the answers, and also give you better support if I don’t know the answer or am away.

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

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