AddH: 'Structure' object has no attribute 'delete_residue'

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-11)
Description
as usuall for my use cases: 'addh hbond true'

Log:
UCSF ChimeraX version: 0.8 (2018-12-11)  
How to cite UCSF ChimeraX  

> open 3d12 fromDatabase pdbe_updated

Summary of feedback from opening 3d12 fetched from pdbe_updated  
---  
note | Fetching compressed mmCIF 3d12 from http://www.ebi.ac.uk/pdbe/entry-
files/download/3d12_updated.cif  
  
3d12 title:  
Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with
its Receptor Ephrin-B3 [more info...]  
  
Chain information for 3d12 #1  
---  
Chain | Description  
A D | Hemagglutinin-neuraminidase  
B E | Ephrin-B3  
  
Non-standard residues in 3d12 #1  
---  
BGC — β-D-glucose  
BMA — β-D-mannose  
GL0 — beta-D-gulopyranose  
GLC — α-D-glucose  
GXL — α-L-galactopyranose  
LXB — 2-(acetylamino)-2-deoxy-beta-D-gulopyranose  
LXZ — 2-(acetylamino)-2-deoxy-alpha-D-idopyranose  
MAN — α-D-mannose  
NAG — N-acetyl-D-glucosamine  
NGA — N-acetyl-D-galactosamine  
NGZ — 2-(acetylamino)-2-deoxy-α-L-glucopyranose  
SO4 — sulfate ion  
  
3d12 mmCIF Assemblies  
---  
1| software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
  

> addh hbond true

Termini for 3d12 (#1) chain D determined from SEQRES records  
Termini for 3d12 (#1) chain A determined from SEQRES records  
Termini for 3d12 (#1) chain E determined from SEQRES records  
Termini for 3d12 (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /D GLU 176, /A GLU 176, /E
SER 29, /B SER 29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /D ALA 603, /A ALA 603, /E GLN
169, /B GLN 169  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /E GLN 169  
Missing OXT added to C-terminal residue /B GLN 169  
1138 hydrogen bonds  
9396 hydrogens added  

> delete #1

> open /Users/lpravda/temp/interactions/pf/3pfn/3pfn_assembly.cif

Summary of feedback from opening
/Users/lpravda/temp/interactions/pf/3pfn/3pfn_assembly.cif  
---  
warning | Missing entity_poly_seq table. Inferring polymer connectivity.  
  
Chain information for 3pfn_assembly.cif #1  
---  
Chain | Description  
A B C D | NAD kinase  
  

> addh hbond true

Termini for 3pfn_assembly.cif (#1) chain C determined from SEQRES records  
Termini for 3pfn_assembly.cif (#1) chain A determined from SEQRES records  
Termini for 3pfn_assembly.cif (#1) chain D determined from SEQRES records  
Termini for 3pfn_assembly.cif (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /D CYS 69, /B CYS 69  
Chain-initial residues that are not actual N termini: /C THR 72, /C THR 86, /C
ALA 116, /C ASP 151, /C TYR 295, /A THR 72, /A GLN 276, /D THR 86, /D GLN 91,
/D ALA 116, /D ALA 232, /D GLN 276, /B GLN 276, /B LEU 296  
Chain-final residues that are actual C termini: /C HIS 427, /A HIS 427, /B HIS
427  
Chain-final residues that are not actual C termini: /C LEU 81, /C MSE 113, /C
ILE 148, /C PRO 292, /A LYS 246, /D LEU 81, /D HIS 89, /D LYS 111, /D GLU 229,
/D LYS 246, /D LEU 425, /B LYS 246, /B PRO 292  
Missing OXT added to C-terminal residue /C HIS 427  
Missing OXT added to C-terminal residue /A HIS 427  
Missing OXT added to C-terminal residue /B HIS 427  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 55, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 160, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, **prot_schemes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 446, in _prep_add  
struct.delete_residue(res)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 43, in __getattr__  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 39, in __getattr__  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'delete_residue'  
  
AttributeError: 'Structure' object has no attribute 'delete_residue'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> delete #1

> open 3pfn

Summary of feedback from opening 3pfn fetched from pdb  
---  
note | Fetching compressed mmCIF 3pfn from
http://files.rcsb.org/download/3pfn.cif  
  
3pfn title:  
Crystal Structure of human NAD kinase [more info...]  
  
Chain information for 3pfn #1  
---  
Chain | Description  
A B C D | NAD kinase  
  
Non-standard residues in 3pfn #1  
---  
UNX — unknown atom or ion  
  
  

> addh hbond true

Termini for 3pfn (#1) chain C determined from SEQRES records  
Termini for 3pfn (#1) chain A determined from SEQRES records  
Termini for 3pfn (#1) chain D determined from SEQRES records  
Termini for 3pfn (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /C THR 72, /C THR 86, /C
ALA 116, /C ASP 151, /C GLY 274, /C TYR 295, /A THR 72, /A GLN 276, /D CYS 69,
/D THR 86, /D GLN 91, /D ALA 116, /D ALA 232, /D GLN 276, /B CYS 69, /B GLN
276, /B LEU 296  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /C LEU 81, /C MSE 113, /C
ILE 148, /C LEU 248, /C PRO 292, /C HIS 427, /A LYS 246, /A HIS 427, /D LEU
81, /D HIS 89, /D LYS 111, /D GLU 229, /D LYS 246, /D LEU 425, /B LYS 246, /B
PRO 292, /B HIS 427  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 55, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 160, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, **prot_schemes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 446, in _prep_add  
struct.delete_residue(res)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 43, in __getattr__  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 39, in __getattr__  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'delete_residue'  
  
AttributeError: 'Structure' object has no attribute 'delete_residue'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/attr_registration.py", line 66, 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-2.4.9
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Hi Lukas,

Thanks for reporting this. Fixed now!

--Eric