[Chimera-users] fitting models into maps
dsouthwo at msg.ucsf.edu
Thu Dec 20 10:47:13 PST 2007
Thanks - this is very informative. I agree it sounds like getting a
cc value from 'fit map into map' is probably the best way. When I
generate the volume from the pdb with eman I'll just have the
molecular weight set to a threshold of 1 and use that threshold when
I run 'fit map into map'. I'll check in to using a std value as well
to see if the numbers are any different. Thanks for your help.
On Dec 19, 2007, at 9:50 PM, Tom Goddard wrote:
> 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
> 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:
>> 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.
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