fit map in map -- also fit a/pix at the same time ?
Hi.
Would it be possible to optimize the a/pix, or scale value when one is fitting either a map in map, or model in map ? Often it seems as if the scale is not 100 % correct between a crystal structure and a cryo-EM reconstructinon, and it would be nice to be able to choose to fit the scale of the EM-map at the same time as the fit rotation and translation.
Best wishes,
Stefan Bäckström Medical Biochemistry and Biophysics Umeå University Sweden
Hi Stefan,
Chimera cannot optimize the volume grid spacing when fitting a molecule model. I agree that would be useful. I'll add it to our requested features list.
http://www.cgl.ucsf.edu/chimera/plans.html
You can do this scale optimization by hand using the volume dialog Coordinates panel to change the voxel size (press the return key after you change the number), then press the Fit button on the Fit in Map dialog. With small scale changes the fit should converge each time and you can quickly try several different scales. The newer Chimera releases (Jan 31, 2008, 1.2492) available on the daily builds page can make a simulated map for your molecule at the desired resolution and report correlation coefficients which is probably better than average map values for this scale optimization.
Tom
participants (2)
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stefan.backstrom＠medchem.umu.se -
Tom Goddard