Terwilliger, Thomas C
terwilliger at lanl.gov
Fri Sep 6 15:32:28 PDT 2013
Hmm... a little hard to tell what the problem is.
So first: autobuild should have refined this model as one of the first things it did. Did it get about the same R that you got when refining it directly with phenix.refine? If no, then have a look at the refinement .eff files (the autobuild one is in AutoBuild_run_1_/TEMP0 unless that was cleaned up) and see what is different.
Next....what happens if you just run phenix.refine to get a map, also take the map from this autobuild run, and look at them along with your model. Is one a lot better than the other?
If you take your best working map and run phenix.fit_loops with this model...how does that do?
All the best,
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Heather L Condurso [condurso at bc.edu]
Sent: Friday, September 06, 2013 3:54 PM
To: PHENIX user mailing list
Subject: [phenixbb] Autobuild
I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this:
Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467
AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013
Deciding if we should continue...
Recent R change per cycle: 0.0
Ending these build cycles as the recent change in R per cycle has been
0.0 and the required value of change is -0.005
and the R is somewhat acceptable at 0.276670644792
All done with build cycles in this region
AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013
All omit/non-omit regions completed
finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013
Finishing AutoBuild Run 162
Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat
AutoBuild Run 162
Summary of model-building for run 162 Fri Sep 6 14:33:40 2013
Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/
Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz
Sequence file: /Users/heather/Desktop/M/m.pir
Best solution on cycle: 2 R/Rfree=0.26/0.33
Summary of output files for Solution 1 from rebuild cycle 2
--- Model (PDB file) ---
--- Model (CIF file) ---
--- Refinement log file ---
--- Model-building log file ---
--- Model-map correlation log file ---
--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT ---
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---
--- Density-modified map coefficients FWT PHWT ---
You might consider making one very good model now with:
My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed.
I am using 1.8.2-1472 if that matters.
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