Tom,

First, I had refine input model before rebuilding turned off.  I thought this meant whether it would refine before doing anything else which I didn't really think was necessary but maybe I was wrong.  I found an autobuild.eff file and it looks like all that was different in my refinement was that I hadn't selected simulated annealing in autobuild and had in refine.  I can run it again with these adjusted parameters to see if I get a better result.  

As for the maps, the refine maps are definitely better than the autobuild maps but not by all that much.  These missing regions are pretty long so fit_loops hasn't been too helpful.  I also had the problem that once I ran fit_loops, I would get an error if I tried to put the new pdb file through refinement.  Something about missing fields but it had only added a residue here and there across many monomers so I gave up.  

I guess what would be helpful to me is how best to use my computing time to try to get autobuild to get me the best possible model it can.  I can input my refined structure but what parameters will make autobuild focus on extending the model to build in the missing regions instead of continually trying to rebuild a model that is already at a CC=0.90 around the built atoms?  

Thanks,
Heather


On Fri, Sep 6, 2013 at 6:32 PM, Terwilliger, Thomas C <terwilliger@lanl.gov> wrote:
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@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Heather L Condurso [condurso@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 \

 seq_file=/Users/heather/Desktop/M/m.pir


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.


Thanks,
Heather

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