coot and mtz interpretation

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Error determining reference matches

Heather L Condurso

28 Aug 2013 28 Aug '13

2:51 p.m.

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? I appreciate any suggestions, Heather

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Nathaniel Echols

28 Aug 28 Aug

2:57 p.m.

On Wed, Aug 28, 2013 at 7:51 AM, Heather L Condurso 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

Heather L Condurso

3:22 p.m.

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 wrote:

...

On Wed, Aug 28, 2013 at 7:51 AM, Heather L Condurso 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Matthew Franklin

3:45 p.m.

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, Matt 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 mailto:[email protected]> wrote:

On Wed, Aug 28, 2013 at 7:51 AM, Heather L Condurso mailto:[email protected]> 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

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Nathaniel Echols

30 Aug 30 Aug

6:25 p.m.

On Wed, Aug 28, 2013 at 8:45 AM, Matthew Franklin 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. -Nat

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Heather L Condurso
Matthew Franklin
Nathaniel Echols