id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4548 ISOLDE: Unparameterised residue detected jimahjr@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/jimahjr/Desktop/MD/2020/model_building_consensus/5w7b_lps.pdb > open > /Users/jimahjr/Desktop/MD/2020/model_building_consensus/cryosparc_P6_J861__localfilter.mrc Opened cryosparc_P6_J861__localfilter.mrc, grid size 240,240,240, pixel 1.07, shown at level 0.203, step 1, values float32 > clipper associate #2 toModel #1 > isolde start > set selectionWidth 4 /Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py:1978: RuntimeWarning: divide by zero encountered in double_scalars self.global_k = scaling_constant/ref_g Done loading forcefield > addh Summary of feedback from adding hydrogens to 5w7b_lps.pdb #1.2 --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 1 hydrogens added > hide HC > isolde restrain ligands #1 > select #1 220 atoms, 221 bonds, 8 residues, 14 models selected > isolde sim start sel Loading residue template for FTT from internal database Loading residue template for MYR from internal database Loading residue template for PO4 from internal database Traceback (most recent call last): File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2727, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 616, in __init__ raise e File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 595, in __init__ isolde.forcefield_mgr) File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1348, in __init__ sim_params, residue_templates) File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1430, in _create_openmm_system raise RuntimeError('Unparameterised residue detected') RuntimeError: Unparameterised residue detected During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 275, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.1.1.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 ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/cmd.py"", line 88, in isolde_sim isolde.start_sim() File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2740, in start_sim self._unparam_mgr._sim_unparam_res_cb() File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/unparameterised.py"", line 207, in _sim_unparam_res_cb self._show_main_frame() File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/unparameterised.py"", line 87, in _update_unparameterised_residues_list by_name, by_comp = ff.find_possible_templates(r) File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/forcefields.py"", line 339, in find_possible_templates template = self._templates[tmpl_name] KeyError: 'GLYCAM_VYNP' KeyError: 'GLYCAM_VYNP' File ""/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/forcefields.py"", line 339, in find_possible_templates template = self._templates[tmpl_name] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.25 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14346.0.0,0) Software: System Software Overview: System Version: macOS 10.14.6 (18G8022) Kernel Version: Darwin 18.7.0 Time since boot: 13 days 20:01 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Thunderbolt Display: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: C02QD5RPF2GC Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort LG UltraFine: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 707NTGY2P607 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 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