[Chimera-users] fitting a protein inside an EM reconstruction

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 12 14:01:56 PDT 2006

Hi Jayant,
Selecting something is not the same as making it movable.  Selecting 
something makes Actions menu items apply to it.  If you want to make 
different models movable/unmovable, use the "Active" checkboxes in the 
Model Panel (Favorites... Model Panel), or various "activate" functions 
in the right side of the Model Panel, or the small checkboxes under the 
Command Line (Favorites... Command Line).

These activation methods determine which models can be moved with the 
mouse or with movement commands like "move" and "turn."

As Tom said, however, the fitting tool requires atoms to be selected.  
Even if only a few atoms are selected, the fitting will move the entire 
model containing the atoms, but maximize the density values at the 
selected atoms.

I hope this helps,

On Oct 12, 2006, at 10:14 AM, jayant_jacques wrote:

>  Hi!
>  I have been trying to fit a protein into an EM reconstruction.
>  methodology
>  I display my protein of interest and EM map on the same window.
>  I select the protein and if I click fit.
>  Problem
>  1. Nothing happens!! If I move the protein the whole frame moves as a 
> whole.
>  2. Also is it possible to click drag the protein into the envelope 
> and then give the fit command such that the program will take over the 
> fitting. As I have 3 proteins to fit into this EM Map.
>  Thanks
>  Jayant
>  Jayasundar Jayant James
>  Postdoc,
>  Department of Veterinary and Comparative Anatomy, Pharmacology 
> and Physiology(VCAPP), Washington state university, Pullman 
> 99164-6520, USA.
>  http://www.chick.com/reading/tracts/0001/0001_01.asp
>  Phone office:335-5937, Cell:1-509-432-5790
> <1963059423 at Middle5.gif>
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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