[phenixbb] Advice about phasing procedure and phase extension in AutoSol-AutoBuild
terwilliger at lanl.gov
Thu Nov 8 10:34:45 PST 2007
>1. can I input known HA-positions into the AutoSol wizard to help
>Hyss find other positions? Does Hyss actually eliminate bogus sites?
>Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a
>B-factor of one, but does not toss them. How does Hyss handle this situation?
As far as I know, you cannot seed hyss with sites.
If you have SAD data, try the autosol wizard which uses Phaser.
Phaser has a good LLG map algorithm for finding addtional sites.
>2. What is the best way to handle phase extension in the Wizards,
>how would one go about this? I would like to fine-tune the
>resolution steps myself as not to jump to far out to higher resolution.
The wizards use the defaults for phase extension in resolve. If you
want to fine-tune the resolution steps you can say,
resolve_command_list=" 's_step 0.05 ' "
Note the 2 sets of quotation marks....
This will use steps of 0.05 A for phase extension
phenix.autobuild --help resolve_command_list
for documentation of this command)
>3. What quality indicators should I look at? A couple of FOMs in the
>resolve runs were in the region of 0.7, but the maps were not
>interpretable and resolve failed to build anything. Anything else I
>should look at?
Best is the R-factor at the end of density modification. If it's
around 0.30 you are doing well. 0.4 is bad, 0.25 is great.
All the best,
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
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