[phenixbb] reflection file utility and use of modified phases in refinement

Engin Ozkan eozkan at stanford.edu
Fri Aug 28 07:16:28 PDT 2009

Hi Tom,

My second question was about autobuild recommending modified phases to 
be used in further refinement.
This is the end of the log file printed by autobuild. See the line for 
"Data for refinement":

Summary of output files for Solution 3 from rebuild cycle 4

---  Model (PDB file)  ---
pdb_file: AutoBuild_run_1_/cycle_best_4.pdb

---  Refinement log file ---
log_refine: AutoBuild_run_1_/cycle_best_4.log_refine

---  Model-building log file ---
log: AutoBuild_run_1_/cycle_best_4.log

---  Model-map correlation log file ---
log_eval: AutoBuild_run_1_/cycle_best_4.log_eval

---  2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT 
refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz

---  Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM 
FreeR_flag ---
hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz

---  Density-modification log file ---
log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod

---  Density-modified map coefficients FP PHIM FOM ---
hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz

If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like 
that's what autobuild suggests.

Thanks again,


On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote:
> Hi Engin,
> I'm not sure about your main question...I hope that Nat or Pavel will
> answer you on that.
> On the use of density-modified phases in refinement: AutoBuild expects
> experimental phases in the data file, with experimental HL coefficients,
> and it by default it will use those HL coefficients in refinement with an
> MLHL target.
> The phase probabilities from resolve statistical density modification are
> pretty accurate, and not inflated, so you could use them in refinement if
> you wanted to. I don't suggest it, however, because the
> density-modification phase information is not fully independent of the
> other information used in refinement (e.g., a flat solvent is implicit in
> your refinement already, so including that through density modification is
> partially redundant).
> ps: I hope AutoBuild doesn't recommend using density-modified phases in
> refinement, so if you could send me the text where it says that, I will
> check that out!
> All the best,
> Tom T
>>> Hi everybody,
>>> I had some trouble with the reflection file utility today. I've been
>>> trying to import Rfree-flag column from one of the mtz's to my combined
>>> mtz, and it never does. The R-free flag is always left out of the output
>>> even when I have it selected. Have you guys seen this (I'm using 147)?
>>> Another question I have is about the output of phenix.autobuild.
>>> Phenix.autobuild tells me to use modified phase probabilities (HLAM,
>>> etc.) in refinement. I am assuming this is density-modified phases. But
>>> I've always thought that this would be bad practice (possibly because of
>>> unrealistically high FOMs and possible flattening of loops, etc, but
>>> maybe resolve does a better job than, say DM). Any ideas on that one?
>>> Thanks,
>>> Engin
>>> --
>>> Engin Özkan
>>> Post-doctoral Scholar
>>> Dept of Molecular and Cellular Physiology
>>> Howard Hughes Medical Institute
>>> Stanford University School of Medicine
>>> ph: (650)-498-7111
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
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Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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