[phenixbb] coot and mtz interpretation

Matthew Franklin mfranklin at nysbc.org
Wed Aug 28 08:45:05 PDT 2013

Hi Heather -

 From your Coot window, you can go to Edit->Preferences, then select the 
"Map Colours" tab in the resulting window.  You should see radio buttons 
for "Coot colours" and "O colours".  The way these work is that you 
select the desired colo(u)r for the positive difference density (e.g. 
green).  The negative contour is then 120 degrees ahead (clockwise) on 
the color wheel if you choose Coot colors, or 120 degrees behind if you 
choose O colors.

It looks to me like you want positive to be green, and negative to be 
red.  So I think you want Coot colors, and positive set to green.  At 
the moment, it appears that you have O colors.

I have no idea if your selections will be kept the next time Phenix 
opens a window for you.  Probably not.

Hope that helps,


On 8/28/13 11:22 AM, Heather L Condurso wrote:
> I can go into map colors and change them to whatever color I want, but 
> if I try and make what I imagine should be + green, then - are royal 
> blue.  The only way I can get red and green is if the - are green, 
> then the positives are red.  I will just pretend royal blue is red for 
> now.  If you come up with anything let me know.
> On Wed, Aug 28, 2013 at 10:57 AM, Nathaniel Echols <nechols at lbl.gov 
> <mailto:nechols at lbl.gov>> wrote:
>     On Wed, Aug 28, 2013 at 7:51 AM, Heather L Condurso
>     <condurso at bc.edu <mailto:condurso at bc.edu>> wrote:
>         I'm having an issue that when I launch coot from the phenix
>         refine gui it loads the pdb and mtz fine, but the FoFc map
>         colors are green and royal blue.  When I open coot first and
>         then load the pdb and mtz files, the FoFc map colors are green
>         and red, but the blobs that were green in the phenix loaded
>         maps are now red and what was royal blue is now green.  Has
>         anyone else had this issue?  I am running a mac with OS X
>         10.6.8 and coot 0.6.1 and phenix 1.8.2-1309.  I have an
>         identical mac running all the same versions and everything
>         loads green and red as expected. Is there a parameter file
>         somewhere that tells coot how to display the phenix maps that
>         may provide a clue as to what is going on?
>     See Preferences->Colors.  If that doesn't seem consistent with
>     what you see in Coot, we may have a bug...
>     -Nat
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Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374

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