[Chimera-users] Query regarding Fit in Map

Tom Goddard goddard at sonic.net
Tue Dec 7 12:05:46 PST 2010

Hi Arun,

   So you just want to measure the correlation for a selected atoms in a 
map, no fit optimization.  This can be done without Python.  Make a 
simulated map with the Chimera "molmap" command, and report the 
correlation with "measure correlation".

     molmap sel 12.5 modelId #5
     measure correlation #5 #0

Here the map is #0, selected atoms are referred to using "sel" and a 
simulated map for those atoms is created as model #5. Results with be in 
Chimera reply log (menu Favorites / Reply Log).

I don't think you want to turn off the "use only data above contour 
level".  If you do it will measure the correlation of the entire box of 
simulated data including all the zeros far from the atom, which probably 
will not match the non-zeros in your map.  If you really want that use 
option "aboveThreshold false" with the measure correlation command.



> Hi Tom,
> Thank you very much for your kind reply. It is quite helpful to know. 
> I am able to run the script and fit a map on to a map. But the problem 
> at had is slightly different. I have got the fits done already  with 
> Flex-EM and I am actually trying to measure (ideally automate it with 
> the Chimera script)  the correlation for the currently selected atoms 
> in the given map using the 'Update' option available in the Fit in Map 
> dialog. I would also like to specify the following option in the script.
> Real-time correlation / average update (turn off within the script)
> Use map simulated from atoms, resolution = value
> use only date above contour level from the first map (turn off within 
> the script)
> optimize correlation
> correlation calculates about mean data value (turn off within the script)
> rotation (turn off within the script)
> shitf (turn off within the script)
> Move whole molecule (turn off within the script)
> I am not sure how to put all this options in a script and calculate 
> the correlation for the currently selected atoms with the Update 
> option. I would greatly appreciate if you could provide me with some 
> more insight on how to change the code specifically. Thanking you.
> with kind regards,
> Arun Prasad
> Tom Goddard wrote:
>>  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 at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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