[Chimera-users] fitting models into maps

Tom Goddard goddard at cgl.ucsf.edu
Wed Dec 19 21:50:58 PST 2007

Hi Dan,

  The Chimera fit model in map tool doesn't give a correlation value.  
To get a correlation requires you have two maps to compare, so first a 
map needs to be calculated from the PDB model that matches the 
resolution of the experimental map.  Although I'd like to have that in 
Chimera, it is not currently there.  I have used the EMAN pdb2mrc 
program to compute the map.  Then you can use the Chimera fit map in map 
tool to get a correlation value, or you could use fit model in map, then 
open the map calculated for the PDB and find the correlation for the 
orientation obtained for the PDB model.

  You're right that reported correlation values depend on some often 
unreported parameters.  First there is the method used for producing a 
map from the PDB model.  Then the correlation depends on the part of the 
volume used.  I would guess this is typically the portion within a 
certain contour level of the PDB map.  What contour level?  Something 
like 1 standard deviation is not sensible since it depends on the size 
of the map (the extent of padding).  Probably a contour level that 
encloses a given volume -- maybe the volume enclosed by the solvent 
excluded surface of the PDB model with a reasonable probe radius.  Would 
be nice if Chimera automated this calculation starting from the fit 
model in map position -- some day, hopefully in 2008.

  Reporting average density value at the atom positions would only make 
sense if the map is normalized.  Maybe reporting that value in standard 
deviations.  But the standard deviation depends on how much empty volume 
surrounds the structure, so that is not very satisfactory.  Chimera 
reports that number so you can compare different fits in the same map -- 
only relative values are meaningful.

  Another value I have seen reported is the number of atoms outside a 
certain contour level of the experimental map.  The fit model in map 
tool reports that in the reply log (Favorites / Reply Log).  Of course 
it depends on how you set the contour level.  Again if you set that as 
some number of standard deviations that depends on the map size.  
Alternatively you could set the contour level so the experimental map 
encloses the expected volume.  Menu entry Tools / Volume Data / Measure 
Volume and Area can help set such a contour level.

  Seems correlation is the most meaningful number.

  You can calculate the standard deviation of a map from its mean in 
newer versions of Chimera with menu entry Tools / Volume Data / Volume 
Mean, SD, RMS.


Daniel Southworth wrote:
> Tom:
> Hi. I'm a post-doc in David Agard's lab and I have a question about 
> the "fit model in map" function in chimera. I'm having some good 
> success fitting crystal structures into my low-resolution em maps 
> using this function once I get a global fit either by hand or using 
> situs. I'm wondering if there is any way to get a correlation value 
> out of the fits or how people typically report on their confidence of 
> the chimera fitting in publications? I know correlation values are 
> often different from program to program so perhaps the best measure is 
> to state the average map value? Any help would be great - thanks.
> Dan

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