[Chimera-users] Query regarding Fit in Map

Tom Goddard goddard at sonic.net
Fri Dec 3 08:17:30 PST 2010

  Hi Arun,

   Yes you can use Fit in Map in a script.  I've attached an example 
Python script.  This script comes from the Chimera Python scripts web 
page but that web site is down right now.  It is necessary to use Python 
rather than a simpler Chimera command script because there is no Chimera 
command to use Fit in Map.  There probably should be, but since Fit in 
Map only does a local optimization you need some way to initially 
position the molecule or map you are fitting.  That is the hard part and 
so there hasn't been much demand for the fitting command.

   The Python code for the Fit in Map dialog is included in all Chimera 
distributions in the directory


You could look at the __init__.py and gui.py to learn what the available 
functions are.  The gui.py (graphical user interface) file shows how 
those functions are called by the dialog.


> Hi all,
> I would like to know whether its possible to automate the operations
> available with 'Fit in Map' tool and its options within a script.
> Actually I would like to calculate the correlation for certain segments
> of the atomic structure and it would be help if I could do it with a
> script rather that the GUI. Any suggestion is greatly appreciated.
> Thank you,
> Arun Prasad
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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