Hi Yu Seon Chung, - I'm not sure I understand why you don't want to use your original file with reflections... - If you start the refinement with non-MTZ file (for example, CNS or SHELX) or the input data was scattered across multiple files (Fobs in one file, HL coefficients in another file, free-R falgs are generated or in third file, etc...), then phenix.refine consolidates all input data and writes it out into a file ending with "_data.mtz". This is the file that you should use in future runs. The data in "_data.mtz" is not processed, that is no sigma or resolution cutoffs are applied to it (even though you used these cutoffs in refinement). - phenix.refine has an option to output calculated structure factors, such as Fmodel, Fcalc_atoms, Fbulk, Fmask, and some other scales, Fobs, free-R flags, etc... The data in this file may be truncated by resolution, sigma, etc. This file is not output by default (export_final_f_model = mtz cns); you need to place "*" in front of cns or mtz to request its output. It is not assumed that you will use this file in next refinement runs. And I presume this is the file you are looking at. Pavel. On 8/26/2008 11:02 AM, YS. Chung wrote:

Hi all,

I have a simple question about the output mtz file from phenix.refine. When I look at the mtz file, it says

***********************************************************

DO NOT USE THIS FILE AS INPUT FOR REFINEMENT!

Resolution and sigma cutoffs may have been applied to FOBS.

***********************************************************

If I have not applied either resolution or sigma cutoffs to FOBS, does that mean that this mtz file is ok to be used for the next round of refinement?

Thank you, Yu Seon Chung _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb