Dear Pavel
2009/3/30 Pavel Afonine
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 gives maps looking like what I would suspect them to. Nice. Thank you for the advice. Best regards, Folmer Fredslund
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