Hi Dan, I think Tom and I have this sorted out now, so you can try the next available nightly build and it should work for you. If you run into further trouble with it, please let us know. Jeff On Tue, Nov 5, 2013 at 8:48 PM, Jeff Headd wrote:

Hi Dan,

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.

Jeff

On Tue, Nov 5, 2013 at 8:12 PM, Dan McNamara wrote:

...

Hello all,

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.

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.

Best, Dan

phenix.autobuild \ data=/home/.../xyz.mtz \ refinement_file=/home/.../xyz.mtz \ input_refinement_labels="FP SIGFP FreeRflag" \ model=/home/.../xyz.pdb \ seq_file=/home/.../xyz.dat \ s_annealing=False \ rebuild_in_place=True \ n_cycle_rebuild_max=3 \ refine_eff_file=/home/.../xyz.eff \ refine_with_ncs=True \ 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 nproc=200 \ general.run_command="/home/.../xyz.sh"

AutoBuild_run_1_/LAST.LOG:

================== Extract refinement strategy and selections =================

Refinement flags and selection counts: individual_sites = True (30132 atoms) torsion_angles = False (0 atoms) rigid_body = True (30120 atoms in 24 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = True (30132 atoms in 4092 groups) tls = True (30120 atoms in 147 groups) occupancies = True (12 atoms) group_anomalous = False

n_use = 30132 n_use_u_both = 30120 n_use_u_iso = 12 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 30132 *** Adding Reference Model Restraints ***

errors.txt:

Sorry:

******************************************************************************** Failed to carry out AutoBuild_build_cycle:

Initial phenix refinement of AutoBuild_run_1_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_1_/LAST.LOG may have additional information... Cannot open file for reading: "/" [Errno 21] Is a directory: '/'

********************************************************************************

Sorry:

******************************************************************************** Failed to carry out AutoBuild_build_cycle:

Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_2_/LAST.LOG may have additional information... Cannot open file for reading: "." [Errno 21] Is a directory: '.'

********************************************************************************

Sorry:

******************************************************************************** Failed to carry out AutoBuild_build_cycle:

Initial phenix refinement of AutoBuild_run_3_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_3_/LAST.LOG may have additional information... Cannot open file for reading: "d" [Errno 2] No such file or directory: 'd'

********************************************************************************

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