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 (type 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: [email protected] 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