[Chimera-users] Fitmap: correlation about the mean for global search

[Tom Goddard]

Hi Michele,

  The Chimera fit list only reports correlation about zero.  This is not great since you optimized for correlation about mean.  A comment in the code mentions this problem.  You can edit a Python file in Chimera to have it report correlation about mean instead.  Change the following code

    def correlation(self):
        return self.stats.get('correlation', None)

to read

    def correlation(self):
        return self.stats.get(‘correlation about mean', None)

in your Chimera distribution in file

	chimera/share/FitMap/search.py

near line 134.  On Mac this file will be in Chimera.app/Contents/Resources/share/FitMap/search.py.

  All our development effort is on ChimeraX now so we will remedy this problem in ChimeraX when we add the fit list to that program, but will not fix it in Chimera.

	Tom


> On Sep 25, 2018, at 9:02 AM, Michele Lunelli wrote:
> 
> Dear people,
> 
> I want to do a global search of an atomic model into an EM map, using the correlation about the mean (cam) as metric. I use a command like this:
> fitmap #0 #1 resolution 6 metric cam search 100 radius 150
> 
> However, only the correlation about zero is reported in the final fit list (and used to rank the solutions). Where can I find the cam values for all the fits?
> 
> Thank you
> Michele
> 
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