id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8195 "raise ValueError(""z_align endpoints must be distinct"")" kristen.browne@… Eric Pettersen "{{{ This may be an issue with the file itself, but wanted to check as have not seen this error when re-run previously: ... File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/cmd.py"", line 50, in preset_cmd run_preset(session, cat, matches[0]) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/cmd.py"", line 71, in run_preset session.presets.preset_function(category, preset)() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/manager.py"", line 60, in cb bi.run_provider(self.session, name, self) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/home/nih3duser/.local/share/ChimeraX/1.6/site-packages/chimerax/nih_presets/__init__.py"", line 22, in run_provider run_preset(session, name, mgr, **kw) File ""/home/nih3duser/.local/share/ChimeraX/1.6/site-packages/chimerax/nih_presets/presets.py"", line 302, in run_preset mgr.execute(cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/manager.py"", line 88, in execute run(self.session, line, log=False) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/coulombic/cmd.py"", line 88, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/coulombic/coulombic.py"", line 99, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status, File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py"", line 26, in add_charges add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py"", line 318, in add_nonstandard_res_charges nonstd_charge(session, tautomer_residues, net_charge, method, status=status) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py"", line 514, in nonstd_charge extras.update(_methylate(na, nbnb, element_counts)) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py"", line 413, in _methylate for pos in bond_positions(nn.coord, 4, 1.1, [na.coord]): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py"", line 78, in bond_positions return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py"", line 158, in tetra_pos pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py"", line 242, in angle_pos xforms = [z_align(atom_pos, bond_pos)] File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/geometry/place.py"", line 567, in z_align raise ValueError(""z_align endpoints must be distinct"") ValueError: z_align endpoints must be distinct Kristen Browne, MSc, MscBMC Contractor - MSC, Inc. | A Guidehouse Company 3D Modeling and Biovisualization Specialist Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, Room 4A60 Rockville, MD 20852 Office 202-253-5228 }}} [attachment:""MARCpeptide.mol2""] " defect feedback normal Structure Analysis all ChimeraX