Hello Kyle, Please use the overall_best.pdb from autobuild and the overall_best mtz file for your model building. You can also check the density modified version of the mtz files. I think the program has some problems with the residue numbering it is not numbering the residues the way you want it to. I recently encountered this. I also think that the cycle_best* files are useless until you are really willing to check each and every step of your model building, but I guess Tom can reflect more on this.I also noticed that you are using an ancient version of Phenix use the latest one its a lot better. hope this helps, Shya
Hi,
I am trying to use the Phenix 1.3 software to solve a structure. After using AutoSol to generate initial phases from a MAD experiment at low resolution (5.0 A), I ran AutoBuild using the solve.mtz output file from AutoSol and a .sca file for higher resolution native data that I had collected from a second crystal. Since my target structure includes both protein and DNA, however, I ran several iterations of AutoBuild changing the parameters for building protein or DNA, including different models, playing with rebuild_in_place, etc. But now that I'm ready to move into manual building and refinement, I have a ton of MTZ files from my AutoBuild runs and I don't know which one(s) I should be using for my maps to guide my model-building, and which one I should consider as "the original" to use in a refinement program like phenix.refine or Refmac. Can anyone help put me on the right path?
Cheers, Kyle
Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb