[Chimera-users] Fitting models into density - meaning of values

Tom Goddard goddard at sonic.net
Wed Oct 30 15:10:38 PDT 2013


Hi Jess,

  The "average map value" that Chimera fitting reports just means the density map value averaged over the center positions of all the fit atoms.  So a higher value means the atoms sit in higher density, and that should be a better fit since the protein density is higher than the solvent density.  Also higher correlation is better.

	Tom



On Oct 29, 2013, at 6:39 PM, Jessica Holien  wrote:

> Thanks Tom - so within my map I can say the higher the value the "better" the fit? Luckily we have a fair bit of biological data which adds to the modelling. I have used the authors "suggested" contour level and knew that the correlation should be around 0.8 (or higher) - which it is for these models at this level. This is my first attempt at EM density fitting and thought Chimera was very user friendly!
> 
> Jess 
> 
> Dr. Jessica Holien, PhD
> Research Officer
> Biota Structural Biology Laboratory
> ACRF Rational Drug Discovery Centre
> St. Vincent's Institute of Medical Research
> 
> Address: 9 Princes St, Fitzroy, Victoria, Australia 3065
> Postal: 41 Victoria St, Fitzroy, Victoria, Australia 3065
> Telephone: +61 3 9288 2685
> 
> ----- Original Message -----
> From: "Tom Goddard" <goddard at sonic.net>
> To: "Jessica Holien" <jholien at svi.edu.au>
> Cc: chimera-users at cgl.ucsf.edu
> Sent: Wednesday, 30 October, 2013 12:22:32 PM
> Subject: Re: [Chimera-users] Fitting models into density - meaning of values
> 
> Hi Jessica,
> 
>  The "average map" value reported by Chimera is only useful for comparing different fits in the same map.  The values in a density map normalized in ways that differ from map to map, so the absolute value is meaningless.  What is sometimes reported in the literature is correlation coefficient, ranging from -1 to 1.  The Chimera fitting will report this if you use the Options button on the Fit Map dialog and enable "Use simulated map … with resolution 23".  The correlation compares a simulated map from your atomic model to the experimental map.  Values like 0.8 and higher are often considered "good".  But unfortunately this is a very poor indicator too for several reasons.  First it depends on the region in space over which the correlation was measured.  In Chimera this will be the grid points within the displayed contour of the simulated map.  (You'll have to show the simulated map using the volume dialog or model panel to see that contour level.)  Higher contour levels use fewer grid points and often give a much higher correlation value.  Another reason this is a poor measure is that it doesn't tell you if there are 5 other very different fits with equally good correlation value.  For a low resolution map like 23 Angstroms, there may be many equally good and very different fits.  The short answer is that it is hard to say if a fit to a low resolution map is good in a convincing way, and the research community does not have standard measures for this.  To make your best effort I would try to produce 2nd and 3rd best fits and see if the 1st best one stands out as a visibly better match (and corresponding higher correlation) than the 2nd and 3rd best fits.
> 
>        Tom
> 
> 
> 
> On Oct 29, 2013, at 5:57 PM, Jessica Holien  wrote:
> 
>> I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks
>> 
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