[phenixbb] MTZ files

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Sun Apr 18 14:08:45 PDT 2010

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,

> 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
> ktd at uchicago.edu
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