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 chimera/share/FitMap 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. Tom

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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users