[phenixbb] annealing omit map

r n ramme29 at yahoo.com
Wed May 16 13:26:21 PDT 2012

Hi all
I found that COOT  is interchanging the traditional colors (green +ve and red -neg) to (green -ve and red +ve), but if read the map using PHENIX GUI, COOT behaves. May be I did some default option wrong in COOT. But even If open the fofc map , COOT interchanges the red for positive 


Sorry for the inconvenience.

 From: r n <ramme29 at yahoo.com>
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org> 
Sent: Wednesday, May 16, 2012 11:16 AM
Subject: [phenixbb] annealing omit map

Hi all

I  have omitted some region manually from the pdb and did annealing - cartesian using phenix.refinment, the resulting map has density (1.2 sigma) in 2fofc and also
seen 2.8 sigma negative density on the omitted region?

any suggestions?


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