[phenixbb] Autobuild
Heather L Condurso
condurso at bc.edu
Fri Sep 6 16:14:15 PDT 2013
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 at 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 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 \
>
> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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