[phenixbb] Judging AutoSol Output
Tom Terwilliger
terwilliger at lanl.gov
Sun Apr 30 12:42:20 PDT 2006
Hi Angela,
Peter makes several excellent points. Here are a few more notes... The file
to look at first is "AutoSol_summary.dat" The final lines in your
AutoSol.output are the same as that file. Here are the useful lines and
how to interpret them
>>Solution # 1 SCORE:110.810151796 Dataset #1 FOM: 0.34 ----------------
110 means 110 sigma above random -> very likely correct
>>Solution 1 using HYSS on ec6046s-peak.sca_ano_1.sca. Dataset #1
>>Dataset number: 1
>>Dataset type: sad
>>Datafiles used: ['ec6046s-peak.sca']
>>Sites: 16 (Already used for Phasing at resol of 2.22) Refined Sites:
>>16 Sites in each NCS group: 4 NCS correlation: 0.661541164
>>Experimental phases in: solve_1.mtz_0
>>Density-modified phases in: resolve_1.mtz_0
>>HA sites (PDB format) in: ha_1.pdb_0
>>Model in: resolve_1.pdb
>> Residues built: 362
Out of 588, this is reasonably good
>> Side-chains built: 11
>> Overall model-map correlation: 0.49
Not that great a correlation, but ok at this stage
>>Scaling logfile in: dataset_1_scale.log
>>HYSS logfile in: ec6046s-peak.sca_ano_1.sca_hyss.log
>>Phasing logfile in: solve_1.prt_0
>>Density modification/build logfile in: resolve_1.log_0
>>
>> Score Type: Resolve CC Resolve R Skew NCS
>>Raw scores: 0.655 0.492 0.157 0.662
>>Z-scores: 38.788 24.380 14.565 33.077
all Z-scores are very high -> strong solution. Particularly convincing is
the NCS correlation of 0.66 and Z-score of 33.
Why didn't solve find all 16 sites? Solve uses a patterson-based method
for sites, AutoSol uses direct methods. Could be that in this case the
patterson method didn't work well.
I hope that helps!
-Tom T
At 04:18 PM 4/24/2006 -0600, agb838 at mail.usask.ca wrote:
>I have some basic questions about the output from Phenix. Basically I
>have a data set that gave a solution, but I am not exactly sure how to
>tell about the quality of the solution from the outputs. The overall
>score is 110. I am not sure exactly what that refers to or how good/bad
>it is. I have attached the AutoSol.output file. Any basic suggestions at
>what I should be looking at, or if this is even the right file, would be
>helpful. The resolve.mtz and resolve.pdb look alright. They are a good
>start, but much improvement is needed. If anyone has some suggestions as
>to how to improve the output, that would also be helpful.
>
>I have also run the data through solve/resolve through the command
>prompt and it repeatedly locates four heavy atom sites (the data set is
>SAD). Yet, when Phenix is used, 16 sites are found. Why the difference
>and how do I tell what is working better and why.
>
>Thank you,
>Angela Hoffort
>
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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
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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