[Chimera-users] Question about Chimera Fit in Map

Tom Goddard goddard at sonic.net
Mon Dec 6 17:37:33 PST 2021

Hi Rakesh,

   Chimera Fit in Map and also the measure correlation command by 
default only compute the cross-correlation within the displayed envelope 
of the first map.  So it should give the masked value you are looking 
for, although the actual value will depend sensitively on the surface 
level of the first map that you choose since that will control which 
grid points near the boundary of your fragment are included.  There is 
no right answer about how tightly to mask and since the correlation 
value is so sensitive to that it is not too meaningful to try to compare 
correlation values although people do it anyways.

   Check out the measure correlation and fit in map docs for more details




On 12/6/2021 5:09 PM, Rakesh Ramachandran wrote:
> Sorry, what I meant was say I am fitting a fragment into a large map, 
> the cross correlation should be calculated only around the fitted 
> region of the fragment, that is any voxels outside the fragment 
> location should not be taken into account in the cross-correlation score.
> I need this because I am fitting fragments of different sizes into a 
> map and I tend to get quite similar cross correlation scores even 
> though principally it should.
> On Mon, Dec 6, 2021 at 5:03 PM Tom Goddard <goddard at sonic.net 
> <mailto:goddard at sonic.net>> wrote:
>     Hi Rakesh,
>       I don't understand what you mean by "length normalized by
>     masking".  Chimera can compute cross-correlation using the Fit in
>     Map panel.  If you are fitting an atomic model to the map it needs
>     to simulate a map from the atomic model  since correlation is
>     between two maps.  You do that using the "Use map simulated from
>     atoms" option in the Fit in Map panel Options pane.
>         Tom
>     On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote:
>>     Hi Tom,
>>        I am using Chimera Fit in Map for EM fitting. Though it does
>>     fit well, I want to calculate a cross correlation score based on
>>     the model map size, that is the cross correlation should be
>>     length normalized by masking the rest of the map.
>>     -- 
>>     Regards
>>     Rakesh Ramachandran
> -- 
> Regards
> Rakesh Ramachandran

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