Error loading structure factors, 1a0m, cannot determine FreeR

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
Command "open 1a0m structureFactors true" produces this error.


Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1a0m structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
notes | 1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
  
  
  
  
| Chain information for 1a0m  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
1.3/A 1.3/B | α-conotoxin [TYR15]-epi  
  
  
  
  
  
  
Non-standard residues in 1a0m #1.3  
  
---  
  
  
  
  
NH2 — amino group  
  
  
  
  
Resolution: 1.0944213038232693  
  
Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 43, in open  
db_models = _fetch_from_database(session, db_id, db_name, db_format, name,
ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 434, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 383, in fetch_cb  
return fetch_shim(session, identifier, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 331, in fetch_mmcif  
mmgr.add_xmapset_from_file(sf_file)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/maps/map_mgr.py", line 276, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/maps/xmapset.py", line 209, in __init__  
self._launch_live_xmap_mgr(crystal_data, fsigf_data)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/maps/xmapset.py", line 353, in _launch_live_xmap_mgr  
num_threads=available_cores())  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/maps/xmapset.py", line 353, in _launch_live_xmap_mgr  
num_threads=available_cores())  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

This is a very old PDB structure so it may not be too important to fix this error.
Additional comments by Tristan in #2002.

[Tristan Croll]

The problem here is that 1a0m has *no* reflections marked as free. The status of each reflection (default, free, unreliable, ...) is marked in the _refln.status column of the .cif file - for this model all reflections are marked 'o' (default). Not that uncommon for pre-2000ish models. To handle it I'll have to add some code to automatically select a new random free set (with a prominent warning) when an existing set cannot be found.

[Tristan Croll]

If an MTZ or cif reflections file does not designate a free set, one will now be automatically created. A warning will be printed to the log, notifying the user that they should save the results to a new MTZ file and use that for all future work with the associated model. I'll upload a new build once I've provided a 'save mtz' command (the Python code is in place, I just have to connect it to the command API).