id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1548 KeyError while writing mmCIF lpravda@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-15) Description Open the attached file and then save it in mmCIF format. Log: Startup Messages --- notes | FYI: command is replacing existing command: ""volume"" FYI: command is replacing existing command: ""color"" UCSF ChimeraX version: 0.8 (2018-12-15) How to cite UCSF ChimeraX > open /Users/pett/rm/1f8p_assembly.cif Summary of feedback from opening /Users/pett/rm/1f8p_assembly.cif --- warnings | Missing entity_poly_seq table. Inferring polymer connectivity. Atom H1 is not in the residue template for TYR #1 in chain A for chain A is incomplete. Ignoring input sequence records as basis for sequence. for chain A is incomplete. Ignoring input sequence records as basis for sequence. for chain A is incomplete. Ignoring input sequence records as basis for sequence. for chain A is incomplete. Ignoring input sequence records as basis for sequence. for chain A is incomplete. Ignoring input sequence records as basis for sequence. 11 messages similar to the above omitted Chain information for 1f8p_assembly.cif --- Chain | Description 1.1/A | neuropeptide Y (PNPY) 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A | neuropeptide Y (PNPY) > save ~/rm/1f8p-test.cif Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 229, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 198, in export result = self.export_func(session, path, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/mmcif/__init__.py"", line 61, in save_file return mmcif_write.write_mmcif(session, path, models=models) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 108, in write_mmcif save_structure(session, f, models, used_data_names) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 508, in save_structure asym_id, entity_id = asym_info[(chain_id, chars)] KeyError: ('A', 'YPSKPDNPGEDAPAEDLARYYSALRHYINLITRQRYX') KeyError: ('A', 'YPSKPDNPGEDAPAEDLARYYSALRHYINLITRQRYX') File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 508, in save_structure asym_id, entity_id = asym_info[(chain_id, chars)] See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: 1f8p_assembly.cif }}} [attachment:""1f8p_assembly.cif""] " defect closed normal Input/Output fixed Eric Pettersen all ChimeraX