[phenixbb] I/O error in writing very large B-factors

[Phil Jeffrey]

This occurs at the end of refinement.  Quite why it's trying to *read* 
from a string with Fortran-esque overflow formatting while in a writing 
step I don't know, but the PDB file gets truncated at
REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP.

The structure is not idyllic, clearly, but I'd like to see the extent of 
the problem rather than just the first atom.  Got to be pretty easy to 
trap for and map to 999.99 either on the way in or out.


Writing refined structure to PDB file:
   /Users/phil/Structures/reference_models/start_refine_001.pdb
n_use            =  21264
n_use_u_iso      =  21264
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  21264
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  21264
Traceback (most recent call last):
   File 
"/usr/local/phenix-1.7.3-928/build/mac-intel-osx/../../phenix/phenix/command_line/refine.py", 
line 11, in <module>
     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
   File 
"/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", 
line 105, in run
     refine_object.write_refined_pdb(f_pdb)
   File 
"/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 
1379, in write_refined_pdb
     ignore_hd = not self.neutron_refinement)
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", 
line 589, in __init__
     ignore_hd = ignore_hd)
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", 
line 504, in __init__
     molprobity_scores=True)
   File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 
1063, in geometry_statistics
     molprobity_scores    = molprobity_scores)
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", 
line 112, in __init__
     self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy)
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", 
line 182, in analyze_clashes
     self.pdb_hierarchy = 
pdb.hierarchy.input(pdb_string=input_str).hierarchy
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/hierarchy.py", line 
1044, in __init__
     source_info=source_info, lines=flex.split_lines(pdb_string))
   File 
"/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/__init__.py", line 
582, in input
     return ext.input(source_info=source_info, lines=lines)
ValueError: string, line 5148:
   ATOM     17  N   ILE A 268     -16.878 -22.262  49.415  1.00****** 
    A    N
   ------------------------------------------------------------^
   not a floating-point number.


Phil Jeffrey
Princeton