id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3509 Chain KeyError opening Phenix CIF file henry.nguyen@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I just tried to open the attached mmCIF file. I converted my pdb to cif using phenix.pdb_as_cif, and then prepared the cif for deposition using mmtbx.prepare_pdb_deposition. The first cif file can be opened and displayed properly. Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.deposit_000.cif Summary of feedback from opening /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.deposit_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 76 Missing entity information. Treating each chain as a separate entity. Atom H1 is not in the residue template for VAL /B:2 Atom H1 is not in the residue template for VAL /D:2 Atom H1 is not in the residue template for VAL /F:2 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 54884 Traceback (most recent call last): File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 150, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 382, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 38, in open return mmcif.open_mmcif(session, data, file_name, **kw) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 88, in open_mmcif for p in pointers] File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 88, in for p in pointers] File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1146, in __init__ self._set_chain_descriptions(self.session) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1349, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) KeyError: 'A' KeyError: 'A' File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1349, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) See log for complete Python traceback. > open > /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.cif Summary of feedback from opening /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 76 Missing entity information. Treating each chain as a separate entity. Atom H1 is not in the residue template for VAL /B:2 Atom H1 is not in the residue template for VAL /D:2 Atom H1 is not in the residue template for VAL /F:2 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 53480 Chain information for full_mNb6_rsr24-coot-5.cif #1 --- Chain | Description A C E | No description available B D F | No description available > hide atoms > show cartoons 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 CorporationHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro10,1 Processor Name: Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB Boot ROM Version: 261.0.0.0.0 SMC Version (system): 2.3f36 Software: System Software Overview: System Version: macOS 10.13.6 (17G13035) Kernel Version: Darwin 17.7.0 Time since boot: 16 days 16:11 Graphics/Displays: Intel HD Graphics 4000: Chipset Model: Intel HD Graphics 4000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0166 Revision ID: 0x0009 Automatic Graphics Switching: Supported gMux Version: 3.2.19 [3.2.8] Metal: Supported, feature set macOS GPUFamily1 v3 NVIDIA GeForce GT 650M: Chipset Model: NVIDIA GeForce GT 650M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Dynamic, Max): 1024 MB Vendor: NVIDIA (0x10de) Device ID: 0x0fd5 Revision ID: 0x00a2 ROM Revision: 3688 Automatic Graphics Switching: Supported gMux Version: 3.2.19 [3.2.8] Metal: Supported, feature set macOS GPUFamily1 v3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No 2217: Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus) UI Looks like: 1680 x 1050 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: P148CHA003927 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: Apple Mini DisplayPort To VGA Adapter Automatically Adjust Brightness: No Adapter Firmware Version: 1.03 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: full_mNb6_rsr24-coot-5.deposit_000.cif }}} [attachment:""full_mNb6_rsr24-coot-5.deposit_000.cif""] " defect closed normal Input/Output fixed Eric Pettersen all ChimeraX