[phenixbb] phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?
Francis E Reyes
Francis.Reyes at Colorado.EDU
Tue May 20 09:07:24 PDT 2008
With option #3, have F+ and F- merged in
exptl_fobs_phases_freeR_flags_xx.mtz? How can I refine with anomalous
flags at this point?
On May 20, 2008, at 9:47 AM, Tom Terwilliger wrote:
> Hi Francis,
> I don't know how to explain the refinement results, but here are
> some comments:
> 1. if you use defaults in autosol, then resolve_xx.mtz will have all
> zeros for the HL coeffs. If you want the HL coeffs you have to say
> 2. I'd recommend refining using the HL coeffs from phaser_xx.mtz or
> solve_xx.mtz, but yes, you can refine against the HL coeffs from
> resolve_xx.mtz and it seems to work ok. Paul Adams did a test a while
> back and the two worked about the same if I recall correctly. My
> logic for using experimental phases in MLHL refinement is that this
> is the independent information that is available; anything from
> density modification as information about where the model is located
> and flatness of solvent mixed in with the experimental information,
> and this duplicates information from the refinement process.
> 3. So in general I'd use exptl_fobs_phases_freeR_flags_xx.mtz from
> autosol, or if you don't build a model in autosol,
> exptl_fobs_phases_freeR_flags.mtz from autobuild.
> All the best,
> -Tom T
> At 09:17 AM 5/20/2008, you wrote:
>> Ok. I think I have a case where I can't refine unless I use density
>> modified experimental phases.
>> I did an autosol run where I specified build=False so I don't have an
>> exptl_fobs_phases_freeR_flags.mtz, but I do have phaser_1.mtz and
>> However, when I refine my model using mlhl my Rfree drops below 30
>> when using resolve_x.mtz and not phaser_x.mtz nor using the original
>> d*trek ref using the same model? Using any of the other mtz's results
>> in Rfree's in the mid 30s. Interestingly refining against the
>> d*trek results in an increase of Rfree with macro cycle?
>> I checked the log file for resolve_x.mtz and although it says it's
>> using the mlhl refinement target, it seems to be using FP, SIGFP (not
>> the HL coefficients that I thought phased refinement would use) as
>> evidenced by the .log file under 'Non-default parameters'. In this
>> section it doesn't read in the HL cofficients? Is there any
>> that it's actually refining against the phases?
>> Any insight as to which mtz to use for final refinement would be
>> What is the refinement target ml_sad?
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
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> Thomas C. Terwilliger
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Francis Reyes M.Sc.
University of Colorado at Boulder
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