Hello!<br><br>I am trying to use Autobuild wizard and it seems that it takes longer time that I expected.<br>That's why I have next questions:<br><br>1. What is "usual" time range estimate for Autobuild run with default parameters if my model has 7 chains with 284 aa in each?<br>
(if I'm running Autobuild on a single machine it does not finish in 3 days or on cluster with usage of 32 processors - in 24 hours)<br><br>2. Do I use phenix comman correctly for using several machines at once? <br><br>
I used /phenix-1.4-89, command line <br><i>phenix.autobuild� data=e239a.hkl seq_file=seq.dat model=model.pdb nproc=32</i><br>
<br><br>In 24 hrs, which is my limit on cluster time, I get next things -<br><font size="1"><font size="2">AutoBuild_run_1_1_/AutoBuild_</font><font size="2">run_1_1.log ends with<br><br></font><i>Setting up to build 5 models to be combined into final model #1<br>
NOTE: input model will be rebuilt in place: nothing will be added or deleted.<br>
Building� 5� models ...<br>Running up to� 32� jobs in parallel...<br>Splitting work into 5 jobs and running 32 at a time with csh in<br>/home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0<br><br>Starting job 1...<br>
Starting job 2...<br>Starting job 3...<br>Starting job 4...<br>Starting job 5...</i><br></font><br>AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with <br><font size="1"><br><i>Copying� refined_pdb_in.pdb� to� composite_model.pdb� in� AutoBuild_run_1_/TEMP0<br>
Beginning merge with current best model:� refined_pdb_in.pdb<br>Merging models: composite_model.pdb refine_1.pdb<br>Refining model:� Build_composite_3.pdb<br>Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb� R/Rfree=0.23/0.25<br>
<br>Rebuilding side chains from� Build_composite_refined_3.pdb</i></font><br><br>or with error <i><br><font size="1">TRIED resolve_extra_huge ...but not OK<br><br>********************************************************************************<br>
Failed to carry out AutoBuild_build_cycle:<br><br><br>********************************************************************************</font></i><br><br>Should I change parameters of the Autobuild which will dramatically reduce time for computations or should I ask for extension of my time for letting the programs to run as it is?<br>
<br>I would give more details if it is needed I just could not think of some other right now. And I would appreciate any advices and suggestions!<br><br><br>Thank you<br>Tanya<br>