[Chimera-users] Query regarding Fit in Map

Tom Goddard goddard at sonic.net
Tue Dec 7 12:16:16 PST 2010

Oops.  Just noticed "measure correlation" is giving an error in Chimera 
1.5 release candidates and daily builds.  I've fixed it and it will work 
in tonight's builds.

Also I noticed that measure correlation was not reporting both 
correlation about mean and correlation without subtracting mean.  
Today's changes will make it report both values.


> 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.
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation
>       Tom
>> 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
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