id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3706 Error opening PDBQT andrew.guy@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.3.0-64-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Error when loading PDBQT file (attached). Error not present in v0.91, but noticed in v1.0. Error present in both Windows 10 and Ubuntu install. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Some installed bundles are out of date. Please update the following bundles: * UI to version 1.2.1 (currently 1.0) * UI to version 1.2 (currently 1.0) > open /home/andrew/Downloads/new1_out.pdbqt Summary of feedback from opening /home/andrew/Downloads/new1_out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK Name = SN00783310 Ignored bad PDB record found on line 4 REMARK 4 active torsions: Ignored bad PDB record found on line 5 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 6 REMARK 1 A between atoms: C_1 and C_5 166 messages similar to the above omitted Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 519, in dropEvent _open_dropped_file(self.session, p) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1721, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/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 ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 382, in collated_open return func(*func_args, **func_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/viewdockx/__init__.py"", line 56, in open return opener(session, data, file_name, True, True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/viewdockx/pdbqt.py"", line 6, in open_pdbqt _extract_metadata(session, f, structures) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/viewdockx/pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values IndexError: list index out of range IndexError: list index out of range File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/viewdockx/pdbqt.py"", line 34, in _extract_metadata structures[model_index].viewdockx_data = vina_values See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 435.21 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Ubuntu 19.10 eoan Architecture: 64bit ELF CPU: 16 AMD Ryzen 7 3700X 8-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 62Gi 4.8Gi 51Gi 707Mi 6.2Gi 56Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 0e:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1) Subsystem: eVga.com. Corp. GP104 [GeForce GTX 1070] [3842:6173] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: new1_1.pdbqt }}} [attachment:""new1_1.pdbqt""] " defect closed normal Input/Output fixed all ChimeraX