[phenixbb] Free-R flag error

S. Saif Hasan sshasan at purdue.edu
Fri Oct 11 06:32:29 PDT 2013


Hello,

I am refining a 3.0 A data set. Initially, I calculated the map at 3.5 A. I have now extended the resolution to 3.0 A, and I imported the FreeR-flags into the 3.0 A .sca file from the 3.5 A file. When I use the 3.0 A .mtz file, phenix.refine gives me this error- 
---------------------------------------------
The MD5 checksum for the R-free flags array summarized above is:
  2ee90dd0a36800bb94370f83daf01698

The corresponding MD5 checksum in the PDB file summarized above is:
  2e1cdfda59def2c4fb80ea6f1e452566

These checksums should be identical but are in fact different. This is
because the R-free flags used at previous stages of refinement are
different from the R-free flags summarized above. As a consequence,
the values for R-free could be biased and misleading.

However, there is no problem if the R-free flags were just extended to
a higher resolution, or if some reflections with no data or that are
not part of the R-free set have been added or removed. In this case,
simply remove the

  REMARK r_free_flags.md5.hexdigest 2e1cdfda59def2c4fb80ea6f1e452566

record from the input PDB file to proceed with the refinement. 

Otherwise it is best to recover the previously used R-free flags
and use them consistently throughout the refinement of the model.
Run this command again with the name of the file containing the
original flags as an additional input.
----------------------------------------
Why does phenix.refine give me this message when I have imported the FreeR-flags from the low resolution file? And what should I do about fixing it?

Thank you for all suggestions.

Saif
Purdue University




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