[phenixbb] phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?
Tom Terwilliger
terwilliger at lanl.gov
Tue May 20 08:47:04 PDT 2008
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
>
>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
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
More information about the phenixbb
mailing list