[phenixbb] Autosol Feedback and questions
terwilliger at lanl.gov
Tue Jan 22 15:18:22 PST 2008
At 03:53 AM 1/2/2008, you wrote:
>Happy new year everybody,
>I had quite a bit of difficulty with a SAD dataset which also showed
>Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to
>refine, AddSOLVE to find more , and both SOLVE and PHASER to solve
>but it did not get to a point where I could do manual building.
>Autosol worked beautifully, the input files were scalepack merged
>data, ha.pdb (from addsolve step), and the sequence. PHASER to solve
>and TEXTAL & RESOLVE with through build option.
>This actually leave me with some confusions / questions:
>1. When I compare the other "solutions", they look like the right
>one, just not good enough. Where exactly is the autosol making a
>difference? Is it the ability of of TEXTAL to build something more
>meaningful when the solution is not good or number of iterations?
Autosol uses the quality of the model built as a score, if any model
is built (R-factor if < 0.40; number of residues built less 2 *
number of chains otherwise).. If no model is built, it uses the
standard 4 or 5 criteria that are printed out on the AutoSol wizard
screen (CC and R-factor for density modification; skew of electron
density histograms, FOM, CC of NCS).
>2. How does PHASER know the different anomalous atoms? Does is use a
>different scaling factor for SE and S?
It can tell by the ratio of anomalous to real scattering
corresponding to each atom.
>3. I see that phenix.refine has been used in the internal runs, I
>have used phenix.refine earlier. But after playing with the side
>chains in Coot, when I tried to use the modified pdb file and
>resolve.mtz, it complained about the good old Free_R flag. However,
>it ran directly in Refmac. Is it a known problem or maybe I did
>something stupid? I could do a dry run and change the read mtz and
>not cns if that would solve the problem.
As Pavel and Ralf have mentioned, this is because AutoSol has tossed
a few (usually blank) reflections from your reflection file when it
created the refinement file
exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without
the "_15" if from AutoBuild
The solution is to either (1) use the refinement file from AutoSol
(exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark
record from the AutoSol/AutoBuild PDB file.
>4. Lastly, is it possible to use multiple processors to run the job?
As Pavel mentioned...we are thinking about this but do not have anything yet.
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
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
More information about the phenixbb