[phenixbb] Tell phenix.autosol to find more heavy atoms?

Tom Terwilliger terwilliger at lanl.gov
Mon May 19 14:56:43 PDT 2008

Hi Francis,

At 02:11 PM 5/19/2008, Francis E Reyes wrote:
>I have a SAD map which is beautiful, but I want to look for more 
>heavy atoms before further refinement...
>Would the proper procedure be....
>SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss:
>phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \
>   sites_file=deriv_hyss_consensus_model.pdb
>This will carry out the usual structure solution process, but will 
>read sites from deriv_hyss_consensus_model.pdb, try both hands, and 
>carry on from there. If you know the hand of the substructure, you 
>can fix it with have_hand=True.

Yes, that is the proper procedure.  I should point out however, that 
Phaser SAD phasing automatically completes the sites (finding more 
after HYSS) so it is likely that if you feed back in the sites from 
the previous run (ha_2,pdb_formatted.pdb or something like that) then 
you probably already have all the sites you are going to get!

>Would there be a PDS friendly way to do this (not necessary though) 
>? i.e. phenix.autobuild after_autosol

Very nice idea...but no, there isn't a nice command like that!
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
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