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
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, [email protected] 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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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 TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
participants (2)
-
agb838＠mail.usask.ca -
Tom Terwilliger