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[ccp4bb] Coot and Density Fit Analysis
 

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CCP4bb <-- 2007 <-- September 2007 <-- 07 September 2007
Previous message:
Subject: Re: Statistics differences
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2007-09-07 		Next message:
Subject: MS method reference
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2007-09-07


Subject: Coot and Density Fit Analysis
From: Andrew Gulick gulick {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2007-09-07
Can someone tell me what the number is that appears with each residue above
the bar in the COOT Density Fit Analysis graph?



I have a structure with good data (resolution=2.3A, Rmerge=5%) but a high
Wilson B of ~60. The structure refines reasonably well; we've gotten the
Rfactor to 18% and Rfree to 22%. It's a previously determined structure
(with new ligands) so we know there is no gross mis-tracing.

If I perform the Density Fit Analysis in COOT, I get a poor looking plot
with significant numbers of red and orange bars. Hovering over a bar gives
the residue and a number that is pretty low (seldom above 0.7) and in
several places there are long stretches of residues that appear fine in the
density where the number in this plot is 0.3.

I see from the documentation and prior CCP4bb postings that perhaps this
results from poor scaling and that I can change the colors of the bars with
the (set-residue-density-fit-scale-factor X) command. If I use the
recommended scale factor (1/4*sigma), the bars get redder. Doing so also
changes the colors and the size of the bars but not the number that appears
above each bar.

My question then is what is the number that appears in this plot? Is it a
correlation coefficient? I have calculated the per residue correlation
coefficients with the CORRELATE program and see much more reasonable values.

Thanks for any suggestions.
Andy


--
Andrew M. Gulick, Ph.D.
-----------------------------------
Hauptman-Woodward Institute
-----------------------------------

CCP4bb navigation

CCP4bb <-- 2007 <-- September 2007 <-- 07 September 2007
Previous message:
Subject: Re: Statistics differences
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2007-09-07 		Next message:
Subject: MS method reference
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2007-09-07


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