Hi Kyle, As Shya says, the overall_best* files are the ones to use for (1) your working model and (2) the best density-modified map. For phenix.refine, use exptl_fobs_phases_freeR_flags.mtz which contains Fobs and sigma, any experimental phase information you have, and freeR flags for refinement. Also yes, definitely move to the current version of phenix which you will like a lot more than the one you have. All the best, Tom T
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
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