id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3093	Error forming missing-structure pseudobonds to internally disconnected residue	goddard@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-16)
Description
Deleting backbone atoms caused this errors, first deleted /A@CA then deleted /A@N.

I know weird steps.  I'm trying to reproduce a ribbon error where residues get deleted by the ribbon does not get updated.


Log:
UCSF ChimeraX version: 0.94.dev202004160103 (2020-04-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1cqt format mmCIF fromDatabase pdb

1cqt title:  
Crystal structure of A ternary complex containing an oca-B peptide, the oct-1
pou domain, and an octamer element [more info...]  
  
Chain information for 1cqt #1  
---  
Chain | Description  
A B | pou domain, class 2, transcription factor 1  
I J | pou domain, class 2, associating factor 1  
M O | DNA (5'-D(*TP*GP*TP*ap*TP*GP*CP*ap*ap*ap*TP*ap*ap*GP*G)-3')  
N P | DNA (5'-D(*ap*CP*CP*TP*TP*ap*TP*TP*TP*GP*CP*ap*TP*ap*C)-3')  
  
1cqt mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
  

> show cartoons

> style stick

Changed 3649 atom styles  

> delete /A@CA

> delete /A@N

Traceback (most recent call last):  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py"", line 258, in execute  
cmd.run(cmd_text)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2848, in run  
result = ci.function(session, **kw_args)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/delete.py"", line 22, in delete  
delete_atoms(session, atoms, attached_hyds=attached_hyds)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/delete.py"", line 39, in delete_atoms  
atoms.delete()  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py"", line 726, in delete  
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
ValueError: No atom in newly disconnected residue lost any bonds!  
  
ValueError: No atom in newly disconnected residue lost any bonds!  
  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py"", line 726, in delete  
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	normal		Core		fixed						all	ChimeraX