id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1962 ViewDockX: Mol2 reader makes duplicate bonds i.ihnatenko@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.9 (2019-05-21) Description Opening a mol2-file generated by GOLD which has two or multiple molecules / conformations of a molecule causes this issue. The file cannot be opened. The problem does not occur in the earlier viersion UCSF ChimeraX version 0.9 (2019-03-18). Log: UCSF ChimeraX version: 0.9 (2019-05-21) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/Irina/PowerFolders/Arbeit/Grundlegende pdb-files/Andere , Debugs/deux résultats.mol2"" Summary of feedback from opening C:/Users/Irina/PowerFolders/Arbeit/Grundlegende pdb-files/Andere , Debugs/deux résultats.mol2 --- warnings | line 120: ignoring section 'SET' line 242: ignoring section 'SET' Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 141, in lambda e, what=what, self=self: self.handle_scheme(what), File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 96, in handle_scheme run(self.session, f'{value}') File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 69, in open _handle_unexpected_keyword_error(e) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 602, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 433, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\\__init__.py"", line 43, in open_file return open_mol2(session, path, file_name, auto_style, atomic) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 5, in open_mol2 p = Mol2Parser(session, stream, file_name, auto_style, atomic) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 81, in __init__ self._make_structure() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 201, in _make_structure s.new_bond(origin, target) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1494, in new_bond return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) TypeError: Bond already exists between these atoms TypeError: Bond already exists between these atoms File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1494, in new_bond return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 23.20.16.4973 OpenGL renderer: Intel(R) HD Graphics 510 OpenGL vendor: Intel }}} " defect closed normal Input/Output fixed all ChimeraX