[phenixbb] coot and mtz interpretation

Nathaniel Echols nechols at lbl.gov
Fri Aug 30 11:25:50 PDT 2013

On Wed, Aug 28, 2013 at 8:45 AM, Matthew Franklin <mfranklin at nysbc.org>wrote:

>  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.

Excellent suggestion.  Heather, does this solve the problem?

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

The Phenix plugin adjusts a few of the settings, but it should leave this
one alone - only the default map colors are set, not the other display
options.  (Although the color for the negative contours will just be
ignored anyway, so I'm taking those out of the Phenix preferences.)  In
general most personal Coot settings should be unmolested - if not, please
let me know.

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