Hi Folmer, I think I dealt with something similar a while ago. Unfortunately I don't remember the details but your description of the problem definitely rings the bells.... If I remember, the problem was some miscommunication between Autobuild and phenix.refine in terms of using incorrect data columns from input mtz file.... Using the right data was a solution. I don't know the answer, but I would try the following which shouldn't take more than 5 minutes or even less. Run phenix.refine to just compute the maps: phenix.refine model.pdb data.hkl strategy=none main.number_of_macro_cycles=1 where data.hkl is your original file with Fobs. This will do not do any refinement but will compute the maps. Now, the map coefficients file (xxx__map_coeffs.mtz) contains two kinds of maps: computed using original unmodified Fobs (labels ending with "_no_fill") and computed using modified Fobs, where missing reflections are filled with DFmodel. To see it, just run this command: phenix.mtz.dump xxx_map_coeffs.mtz So I would suggest to compare these two kinds of maps. If this doesn't give you any clue, the next question is: does your input data file (the one that is used in Autobuild) contain HL coefficients? If it does, then try why I suggested above but run phenix.refine slightly different: phenix.refine model.pdb data.hkl strategy=none main.number_of_macro_cycles=1 use_experimental_phases=false and have a look at the maps once again. If this does not help, and no-one else suggests anything else to try out, you may want to send me your input files and I will try to find what's going on. All files will be treated confidentially. Pavel. On 3/28/09 4:29 AM, Folmer Fredslund wrote:

Dear all,

In phenix.refine (1.4-3) my electron density maps look weird. I get beautiful density for a helix that is missing from the current model, but absolutely horrible density for the rest of the molecule. Any ideas what is going on? Maps from automr look fine and the density modified map from autobuild also look fine, whereas the autobuild map from refinement has the same features.

Any ideas what is going on? I am running all programs with default parameters.

Best regards, Folmer Fredslund _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb