id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2005 Error loading structure factors, 1a0m, cannot determine FreeR goddard@… Tristan Croll "{{{ 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 }}} " defect closed normal Volume Data 0.9 fixed all ChimeraX