Hi Francis, If you want to refine using anomalous data, then it is best to use your original dtrek data. You can supply the freeR_flags from exptl_fobs_phases_freeR_flags.mtz if you want. Or you can generate freeR flags from your original data -- but then you must use these freeR flags from the beginning and redo everything involving model-building.. All the best -Tom T At 10:07 AM 5/20/2008, you wrote:

Thanks Tom

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?

Thanks

FR

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

hl_in_resolve=true

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 resolve_1.mtz.

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 original 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 indication that it's actually refining against the phases?

Any insight as to which mtz to use for final refinement would be suggested.

Thanks

FR

P.S.

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 Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB