[Chimera-users] fitting models into maps

Daniel Southworth 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  
> 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.
>    Tom
> 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

More information about the Chimera-users mailing list