[phenixbb] Autosol Feedback and questions

Tom Terwilliger terwilliger at lanl.gov
Tue Jan 22 15:18:22 PST 2008

Hi Partha,

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.

-Tom T

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

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