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Opened 3 years ago
Last modified 3 years ago
#8725 assigned defect
SEQCROW: various errors
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/asiawolak/Downloads/5iih (1).pdb" format pdb
5iih (1).pdb title:
Crystal structure of equine serum albumin In the presence of 2.5 MM zinc At pH
7.4 [more info...]
Chain information for 5iih (1).pdb #1
---
Chain | Description | UniProt
A | serum albumin | ALBU_HORSE
Non-standard residues in 5iih (1).pdb #1
---
SO4 — sulfate ion
ZN — zinc ion
> ui tool show "Swap Transition Metal Ligands"
> select /A:601@ZN
1 atom, 1 residue, 1 model selected
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 582, in do_change_element
residue.change_element(targ,
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 582, in do_change_element
residue.change_element(targ,
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
See log for complete Python traceback.
> hide target m
> close
> open "/Users/asiawolak/Downloads/5iih (1).pdb" format pdb
5iih (1).pdb title:
Crystal structure of equine serum albumin In the presence of 2.5 MM zinc At pH
7.4 [more info...]
Chain information for 5iih (1).pdb #1
---
Chain | Description | UniProt
A | serum albumin | ALBU_HORSE
Non-standard residues in 5iih (1).pdb #1
---
SO4 — sulfate ion
ZN — zinc ion
> select /A:601@ZN
1 atom, 1 residue, 1 model selected
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 582, in do_change_element
residue.change_element(targ,
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 582, in do_change_element
residue.change_element(targ,
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
RuntimeError: cannot remove 1 hydrogens from an atom with 0 hydrogens
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/geometry.py", line 4574, in change_element
raise RuntimeError(
See log for complete Python traceback.
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 588, in do_change_element
residue.update_chix(res)
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/residue_collection.py", line 310, in update_chix
self.refresh_chix_connected(chix_residue)
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/residue_collection.py", line 350, in refresh_chix_connected
pbg =
chix_residue.structure.pseudobond_group(chix_residue.structure.PBG_METAL_COORDINATION,
create_type='normal')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1835, in pseudobond_group
return f(self._c_pointer, name.encode('utf-8'), create_arg)
TypeError: Group type mismatch
TypeError: Group type mismatch
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1835, in pseudobond_group
return f(self._c_pointer, name.encode('utf-8'), create_arg)
See log for complete Python traceback.
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
[_lots_ of these deleted]
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
WARNING AaronTools.atoms.Atom.copy
No copy method for <class 'chimerax.atomic.molobject.Atom'>: in-place
changes may occur
Traceback (most recent call last):
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/structure_editing.py", line 588, in do_change_element
residue.update_chix(res)
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/residue_collection.py", line 310, in update_chix
self.refresh_chix_connected(chix_residue)
File "/Users/asiawolak/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/residue_collection.py", line 350, in refresh_chix_connected
pbg =
chix_residue.structure.pseudobond_group(chix_residue.structure.PBG_METAL_COORDINATION,
create_type='normal')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1835, in pseudobond_group
return f(self._c_pointer, name.encode('utf-8'), create_arg)
TypeError: Group type mismatch
TypeError: Group type mismatch
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1835, in pseudobond_group
return f(self._c_pointer, name.encode('utf-8'), create_arg)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11B0002RZE/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 26 dni, 13 godzin i 59 minut
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.6.1
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: various errors |
follow-up: 2 comment:2 by , 3 years ago
Joanna, Thanks for reporting this. For changing the zinc to something else, the geometry I'd recommend here is "do not change", which is at the top of the list. To avoid the "cannot remove hydrogens" error, you would also need to choose a geometry with at least 5 atoms (the zinc has 5 coordination bonds), as it will try to delete hydrogens to get down to the appropriate number of bonds. None of the 5-bond geometries look like a good fit for this, which is why I'm recommending "do not change". The warnings about "in-place changes" will be finally removed in the next update. I've been trying to get rid of those for a while, and I just figured out they aren't coming from the function they say they are coming from. With the error related to the metal coordination pseudobonds, I guess the existing coordination pseudobonds were created in a way that lets them change if the atomic coordinate set changes. I did not account for this possibility, but it will be fixed soon. For what it's worth, choosing "do not change" for the geometry when changing elements will bypass all the code that causes the error about removing hydrogens, the warnings about copying atoms, and the TypeError for the pseudobond group. Tony On Mon, Mar 27, 2023 at 1:03 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
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Reported by Joanna Wolak