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 density? Sorry for the inconvenience. ________________________________ From: r n To: "[email protected]" 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? Rab _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb