Hi Emily,
It could be a scaling issue. Coot has a parameter under
Extensions...Refine...Set Density Fit Graph Weight... Making this value
smaller will make the bars shorter and greener. So if the two maps (or
coefficients) are on different scales, you will need different values of the
Set Density Fit Graph Weight to make the two sets look similar.
Jack
On Feb 20, 2015, at 9:11 AM, Emilia C. Arturo (Emily) wrote:
Thank you for the multiple kind off-list responses I received regarding how to
interpret map colors in Coot. I'm very grateful for the references, but it
seems that I did not state my issue clearly :-) What I was referring to was the
tool that Coot has under Validate Density Fit analysis. The tool outputs
graphs like the ones I'm pasting below. Both sets of graphs were generated from
the same pdb file, but the very-red bar graphs were calculated using the map
coefficients phenix had generated along with this model, while the mostly green
bar graphs pasted separately below, showing bars for the same stretch of
residues in each chain, were generated using the feature enhanced map that
phenix generated from this same model.Screen Shot 2015-02-20 at 9.56.22
AM.pngScreen Shot 2015-02-20 at 9.56.49 AM.png How do I interpret the fact
that the FEM and 2Fo-Fc maps give such different fits for the same model using
this type of analysis? ...or are the fits really that different (and maybe
green versus red is not as big as the visual cue would have me assume)?
Emily.
On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily)
ec...@drexel.edumailto:ec...@drexel.edu wrote:
Hello all.
I'd like to understand what it is I'm looking at when I use Coot's density fit
analysis tool. I recognize that there was a post related to this topic on the
Coot bb a while ago --the discussion was on how to interpret the red-ness or
green-ness of the density fit plot
(https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)--but
--but it doesn't seem the issue was resolved then (i.e. what does 'red' really
mean? is it ...bad?). Now I have more to ask that involves my using
phenix-generated FEMs to build in Coot.
So what I've done is the following: I adjust my model in Coot, using a
phenix-generated FEM as the map for fitting, then refine with phenix, and using
the refined pdb and reflections file, I use phenix to generate a new FEM. Then
I repeat. At some point I learned about Coot's density fit analysis tool and
took a look at how my model fits. If the map that is selected in the sidebar of
Coot is a FEM, then the density fit analysis plot looks mostly green everywhere
- fine. If, however, I select as my map in the Coot sidebar the 2Fo-Fc that
phenix had generated along with the latest refined model--the one I'm examining
with the density fit analysis tool--then Coot's density fit analysis plot looks
red (with values ~ 0.3), with splashes of orange, barely any green or yellow
(with values ~ 0.3), almost everywhere.
So these are my questions: What are the units of the density fit values? i.e.
What is the calculation that's done? I'm surprised that the FEM-dependent
density fit graphs look so different (i.e. so green) relative to the graphs
generated if my map is set to the 2Fo-Fc from the loaded model; both maps came
from the same model. In fact, I got worried, but then I realized that I don't
actually understand the red-ness and green-ness. I'm quite new to the business
of crystallography so any input is welcome regarding the use of FEMs and
density fit analyses.
Emily.
Ph.D. program in Biochemistry, Drexel Univ. College of Medicine
Jaffe lab, Fox Chase Cancer Center
Philadelphia, PA