[phenixbb] Advice about phasing procedure and phase extension in AutoSol-AutoBuild

Tom Terwilliger terwilliger at lanl.gov
Thu Nov 8 10:34:45 PST 2007

Hi Carsten,

>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,
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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