Re: [Chimera-users] Query regarding Fit in Map
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#correlati... 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. Tom
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#correlati...
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (1)
-
Tom Goddard