[phenixbb] Autobuild

Terwilliger, Thomas C terwilliger at lanl.gov
Fri Sep 6 15:32:28 PDT 2013

Hi Heather,

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,
Tom T

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)  ---

pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb

---  Model (CIF file)  ---

cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif

---  Refinement log file ---

log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine

---  Model-building log file ---

log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log

---  Model-map correlation log file ---

log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval

---  2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT ---

refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz

---  Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---

refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz

---  Density-modified map coefficients FWT PHWT ---

denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz

You might consider making one very good model now with:

phenix.autobuild \

 data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \

 model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \

 rebuild_in_place=True \


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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