id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20262 ISOLDE restraints: cannot access local variable 'template_us' where it is not associated with a value chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/zeini/Desktop/IZ10-1/3DVA_IZ10-1/cryosparc_P1_J239_component_000/emready_component000/J239_component_000_frame_000.mrc_emready.mrc Opened J239_component_000_frame_000.mrc_emready.mrc as #1, grid size 400,400,400, pixel 0.76, shown at level 1.02, step 2, values float32 > open /Users/zeini/Downloads/SD_final.cif- > coot-0_D402V_real_space_refined_000.cif Summary of feedback from opening /Users/zeini/Downloads/SD_final.cif- coot-0_D402V_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 358 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""42"" on line 183 Bad residue range for struct_conf ""43"" on line 184 Bad residue range for struct_conf ""44"" on line 185 Bad residue range for struct_conf ""45"" on line 186 Bad residue range for struct_conf ""46"" on line 187 Invalid residue range for struct_conf ""47"": residue in non-polymer entity ""B"", on line 188 Invalid residue range for struct_conf ""48"": residue in non-polymer entity ""B"", on line 189 Invalid residue range for struct_conf ""49"": residue in non-polymer entity ""B"", on line 190 Invalid residue range for struct_conf ""50"": residue in non-polymer entity ""B"", on line 191 Invalid residue range for struct_conf ""51"": residue in non-polymer entity ""B"", on line 192 24 messages similar to the above omitted Bad residue range for struct_conf ""89"" on line 230 Bad residue range for struct_conf ""90"" on line 231 Bad residue range for struct_conf ""93"" on line 234 Bad residue range for struct_conf ""94"" on line 235 Bad residue range for struct_conf ""95"" on line 236 3 messages similar to the above omitted Missing or incorrect sequence information. Inferred polymer connectivity. Atom HO5' is not in the residue template for DG /H:1 Atom HO5' is not in the residue template for DC /T:-11 Skipping chem_comp category: Missing column 'type' on line 40018 Skipping chem_comp category: Missing column 'type' on line 40114 Skipping chem_comp category: Missing column 'type' on line 40431 Chain information for SD_final.cif-coot-0_D402V_real_space_refined_000.cif #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available P | No description available T | No description available > hide #!1 models > show #!1 models > hide #!2 models > volume flip #1 Opened J239_component_000_frame_000.mrc_emready.mrc z flip as #3, grid size 400,400,400, pixel 0.76, shown at step 1, values float32 > show #!2 models > clipper associate #3 toModel #2 Opened J239_component_000_frame_000.mrc_emready.mrc z flip as #2.1.1.1, grid size 400,400,400, pixel 0.76, shown at level 5.62, step 1, values float32 Chain information for SD_final.cif-coot-0_D402V_real_space_refined_000.cif #2.2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available P | No description available T | No description available > isolde restrain basepairs #1.2/P-T > isolde restrain distances #1.2/P-T Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 322, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/zeini/Library/Application Support/ChimeraX/1.11/lib/python/site- packages/chimerax/isolde/restraints/cmd.py"", line 46, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/Users/zeini/Library/Application Support/ChimeraX/1.11/lib/python/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 573, in restrain_atom_distances_to_template template = template_us[0] ^^^^^^^^^^^ UnboundLocalError: cannot access local variable 'template_us' where it is not associated with a value UnboundLocalError: cannot access local variable 'template_us' where it is not associated with a value File ""/Users/zeini/Library/Application Support/ChimeraX/1.11/lib/python/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 573, in restrain_atom_distances_to_template template = template_us[0] ^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac21,1 Model Number: Z12Q000EXAB/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.41.1 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 56 days, 3 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 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