<div dir="ltr">Hi Dan,<div><br></div><div>I don't think I've ever tried to use a reference model in AutoBuild. I'll test it out and talk with Tom about what the problem is, and let you know when we have it sorted it.</div>
<div><br></div><div>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 8:12 PM, Dan McNamara <span dir="ltr"><<a href="mailto:dem@ucla.edu" target="_blank">dem@ucla.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr">Hello all,<br><br>I'm hoping to troubleshoot a problem with autobuild and the use of a reference model. Autobuild has been always failing once it gets to the initial refinement step and attempts to add reference model restraints.� I've included my autobuild parameterization. Refinement is where it dies and the contents of LAST.LOG and my error log file are below too. <br>
<br>I'm not sure how to get the reference model file location properly interpreted. I even tried manually moving the reference PDB into the AutoBuild_run_X_/ and TEMP0/ folders as they're generated to no avail.<br>
<br>Best,<br>Dan<br><br><br>phenix.autobuild \<br>������� data=/home/.../xyz.mtz \<br>������� refinement_file=/home/.../xyz.mtz \<br>������� input_refinement_labels="FP SIGFP FreeRflag" \<br>������� model=/home/.../xyz.pdb \<br>
������� seq_file=/home/.../xyz.dat \<br>������� s_annealing=False \<br>������� rebuild_in_place=True \<br>������� n_cycle_rebuild_max=3 \<br>������� refine_eff_file=/home/.../xyz.eff \<br>������� refine_with_ncs=True \<br>
������� model_building.reference_model=/home/.../def.pdb \�� #I have also tried locations like ../def.pdb and def.pdb that give Errno 21 or Errno 2 below<br>������� nproc=200 \<br>������� general.run_command="/home/.../xyz.sh"<br>
<br>AutoBuild_run_1_/LAST.LOG:<br><br>================== Extract refinement strategy and selections =================<br><br>Refinement flags and selection counts:<br>� individual_sites������ =� True (30132 atoms)<br>� torsion_angles�������� = False (0 atoms)<br>
� rigid_body������������ =� True (30120 atoms in 24 groups)<br>� individual_adp�������� = False (iso = 0 aniso = 0)<br>� group_adp������������� =� True (30132 atoms in 4092 groups)<br>� tls������������������� =� True (30120 atoms in 147 groups)<br>
� occupancies����������� =� True (12 atoms)<br>� group_anomalous������� = False<br><br>n_use����������� =� 30132<br>n_use_u_both���� =� 30120<br>n_use_u_iso����� =� 12<br>n_use_u_aniso��� =� 0<br>n_grad_site����� =� 0<br>
n_grad_u_iso���� =� 0<br>n_grad_u_aniso�� =� 0<br>n_grad_occupancy =� 0<br>n_grad_fp������� =� 0<br>n_grad_fdp������ =� 0<br>total number of scatterers =� 30132<br>*** Adding Reference Model Restraints ***<br><br><br><br>
<br>errors.txt:<br><br>Sorry:<br>********************************************************************************<br>Failed to carry out AutoBuild_build_cycle:<br><br>Initial phenix refinement of AutoBuild_run_1_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting...<br>
/home/.../AutoBuild_run_1_/LAST.LOG may have additional information...<br>Cannot open file for reading: "/"<br>� [Errno 21] Is a directory: '/'<br>********************************************************************************<br>
<br>Sorry:<br>********************************************************************************<br>Failed to carry out AutoBuild_build_cycle:<br><br>Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting...<br>
/home/.../AutoBuild_run_2_/LAST.LOG may have additional information...<br>Cannot open file for reading: "."<br>� [Errno 21] Is a directory: '.'<br>********************************************************************************<br>
<br>Sorry:<br>********************************************************************************<br>Failed to carry out AutoBuild_build_cycle:<br><br>Initial phenix refinement of AutoBuild_run_3_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting...<br>
/home/.../AutoBuild_run_3_/LAST.LOG may have additional information...<br>Cannot open file for reading: "d"<br>� [Errno 2] No such file or directory: 'd'<br>********************************************************************************<br>
</div><br></div>
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