[Chimera-users] Fit models to map

Thomas Goddard goddard at cgl.ucsf.edu
Mon Dec 4 10:11:04 PST 2006

Hi Hernando,

  The details about how fitting models in maps is works are described in
the Chimera manual.


You can display the manual page by pressing the Help button on the Fit
Models in Maps dialog.

  Briefly, it does not compute a density from the atomic model -- that
would require you specify a resolution if you wanted a meaningful cross
correlation value.  It simply looks at interpolated density values at
the atom positions and maximizes their sum.  It uses gradient descent
and typically translates by no more than about the molecule radius and
rotates by no more than about 90 degrees.  There are no coded limits
though.  For step sizes and convergence criteria see the manual.

  A few weeks ago I wrote some code to fit a map in another map and report
the correlation coefficient:


This will be part of Chimera in the next snapshot releases.  It still does
not compute a density from a PDB model so you would have to do that with
an external program.  We will add that capability in the future.


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