[phenixbb] MTZ files

Thomas C. Terwilliger terwilliger at lanl.gov
Sun Apr 18 18:46:19 PDT 2010

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,


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
>>> ktd at uchicago.edu
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list