id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2701 handle sub packages split between user and app install areas pett@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) try to launch a matchmaker alignment Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_Alignments-1.0-py3-none-any.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\adele\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_alignments-1.0-py3-none- any.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.9 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Alignments==1.0) (0.91) Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Alignments==1.0) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Alignments==1.0) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-MouseModes>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- UI>=1.0->ChimeraX-Alignments==1.0) (1.0) Installing collected packages: ChimeraX-Alignments Successfully installed ChimeraX-Alignments-1.0 Lock 2942254612104 acquired on C:\Users\adele\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock Lock 2942254612104 released on C:\Users\adele\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock > open C:/Users/adele/Desktop/MesArticles/InProgress/Docking/pdb2vla.ent pdb2vla.ent title: Crystal structure of restriction endonuclease bpuji recognition domain In complex with cognate DNA [more info...] Chain information for pdb2vla.ent #1 --- Chain | Description A | BPUJI L | 5'-D(*GP*GP*TP*ap*CP*CP*CP*GP*TP*GP *GP*A)-3' M | 5'-D(*TP*CP*CP*ap*CP*GP*GP*GP*TP*ap *CP*C)-3' Non-standard residues in pdb2vla.ent #1 --- NA — sodium ion PG6 — 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane > open > C:\Users\adele\Desktop\MesArticles\InProgress\Docking\NBI_modelchoisi.pdb Chain information for NBI_modelchoisi.pdb #2 --- Chain | Description | No description available > open > C:\Users\adele\Desktop\MesArticles\InProgress\Docking\v11plus_unbound.pdb Summary of feedback from opening C:\Users\adele\Desktop\MesArticles\InProgress\Docking\v11plus_unbound.pdb --- warning | CONECT record for nonexistent atom: 313 Chain information for v11plus_unbound.pdb #3 --- Chain | Description A | No description available B | No description available > mmaker #2 to #1 showAlignment true Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2854, in run _used_aliases=used_aliases, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 3400, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py"", line 603, in cmd_match from chimerax.seqalign import sim_matrices ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign' (C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\seqalign\\__init__.py) ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign' (C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\seqalign\\__init__.py) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py"", line 603, in cmd_match from chimerax.seqalign import sim_matrices See log for complete Python traceback. > mmaker #2 to #1 showAlignment true Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 258, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2854, in run _used_aliases=used_aliases, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 3400, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py"", line 603, in cmd_match from chimerax.seqalign import sim_matrices ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign' (C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\seqalign\\__init__.py) ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign' (C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\seqalign\\__init__.py) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py"", line 603, in cmd_match from chimerax.seqalign import sim_matrices See log for complete Python traceback. OpenGL version: 3.3.0 - Build 24.20.100.6299 OpenGL renderer: Intel(R) HD Graphics 520 OpenGL vendor: Intel }}} " defect closed major 1.1 Tool Shed duplicate Conrad Huang all ChimeraX