Build Structure executing old (Chimera1) code

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-12)
Description
Tried phosphorylating a serine with Build Structure.  Changing the H to a P worked, but then trying to change the first H on the new P to an O gave this error when I pressed Apply in Build Structure.  The O got added, but looks like the bond length is wrong, probably due to this error.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-02-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3ajo format mmCIF fromDatabase pdb

3ajo title:  
Crystal structure of wild-type human ferritin H chain [more info...]  
  
Chain information for 3ajo #1  
---  
Chain | Description  
A | Ferritin heavy chain  
  
Non-standard residues in 3ajo #1  
---  
MG — magnesium ion  
  
3ajo mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> addh

Summary of feedback from adding hydrogens to 3ajo #1  
---  
notes | Termini for 3ajo (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A THR 5  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLY 176  
806 hydrogen bonds  
Adding 'H' to /A THR 5  
/A GLY 176 is not terminus, removing H atom from 'C'  
1815 hydrogens added  
  

> show :SER

> select /A:36@HG

1 atom, 1 model selected  

> toolshed show "Build Structure"

> build modify /A:36@HG P 4 geometry tetrahedral name P1 resName UNK

> select /A:36@H11

1 atom, 1 model selected  

> build modify /A:36@H11 O 4 geometry tetrahedral name O1

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/build_structure/tool.py", line 137, in <lambda>  
apply_but.clicked.connect(lambda checked: self._ms_apply_cb())  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/build_structure/tool.py", line 298, in _ms_apply_cb  
run(self.session, cmd)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/build_structure/cmd.py", line 19, in cmd_modify_atom  
return modify_atom(*args, **kw)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/build_structure/mod.py", line 156, in modify_atom  
else gen_atom_name(hydrogen, atom.residue)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/struct_edit.py", line 252, in gen_atom_name  
if name not in residue.atomsMap:  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Residue' object has no attribute 'atomsMap'  
  
AttributeError: 'Residue' object has no attribute 'atomsMap'  
  
File "/Users/goddard/Desktop/ChimeraX Feb 12
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.