<div dir="ltr">Tom,<div><br></div><div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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? </div>
<div><br></div><div>Thanks,</div><div>Heather</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Sep 6, 2013 at 6:32 PM, Terwilliger, Thomas C <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Heather,
<div><br>
</div>
<div>Hmm... a little hard to tell what the problem is.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>If you take your best working map and run phenix.fit_loops with this model...how does that do?</div>
<div><br>
</div>
<div>All the best,</div>
<div>Tom T</div>
<div><br>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] on behalf of Heather L Condurso [<a href="mailto:condurso@bc.edu" target="_blank">condurso@bc.edu</a>]<br>
<b>Sent:</b> Friday, September 06, 2013 3:54 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> [phenixbb] Autobuild<br>
</font><br>
</div><div><div class="h5">
<div></div>
<div>
<div dir="ltr">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:
<div><br>
</div>
<div>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Deciding if we should continue...</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Recent R change per cycle: 0.0</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
<br>
</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Ending these build cycles as the recent change in R per cycle has been </p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">0.0 and the required value of change is -0.005</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">and the R is somewhat acceptable at 0.276670644792</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">All done with build cycles in this region</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">All omit/non-omit regions completed</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Finishing AutoBuild Run 162</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild Run 162</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Summary of model-building for run 162 Fri Sep 6 14:33:40 2013</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Sequence file: /Users/heather/Desktop/M/m.pir</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Best solution on cycle: 2 R/Rfree=0.26/0.33</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Summary of output files for Solution 1 from rebuild cycle 2</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Model (PDB file) ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Model (CIF file) ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Refinement log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Model-building log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Model-map correlation log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">--- Density-modified map coefficients FWT PHWT ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">You might consider making one very good model now with: </p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">phenix.autobuild \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier"> data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier"> model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier"> rebuild_in_place=True \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier"> seq_file=/Users/heather/Desktop/M/m.pir</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px">
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<div>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. </div>
</div>
<div><br>
</div>
<div>I am using 1.8.2-1472 if that matters.</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Heather</div>
</div>
</div>
</div></div></div>
</div>
</div>
</div>
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<br></blockquote></div><br></div>