swapaa: DunbrackRotamerLibrary' object has no attribute 'display_name'

[samira.alsadi@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-122-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6rc202305021906 (2023-05-02 19:06:00 UTC)
Description
tried to change 2 residue side chains with the swapaa command following the syntax shown in the user guide.

i tried: 
swapaa #3:469,218 gln,met
swapaa #3:469,218 seq:QM

but log showed the same error.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8j03

Summary of feedback from opening 8j03 fetched from pdb  
---  
note | Fetching compressed mmCIF 8j03 from
http://files.rcsb.org/download/8j03.cif  
  
8j03 title:  
Human KCNQ2(F104A)-CaM-PIP2-CBD complex in state I [more info...]  
  
Chain information for 8j03 #1  
---  
Chain | Description | UniProt  
A D G I | Potassium voltage-gated channel subfamily KQT member 2 | KCNQ2_HUMAN
64-703  
E F H J | Calmodulin-1 | CALM1_HUMAN 1-149  
  
Non-standard residues in 8j03 #1  
---  
P0T — cannabidiol
((1'R,2'R)-5'-methyl-4-pentyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,6-diol)  
  

> close

> open 8p0q

Summary of feedback from opening 8p0q fetched from pdb  
---  
note | Fetching compressed mmCIF 8p0q from
http://files.rcsb.org/download/8p0q.cif  
  
8p0q title:  
Crystal structure of AaNGT complexed to UDP and a peptide [more info...]  
  
Chain information for 8p0q #1  
---  
Chain | Description | UniProt  
A B | Adhesin | A0A3M6PNT1_AGGAP 1-621  
C D | PHE-GLY-ASN-TRP-THR-THR |  
  
Non-standard residues in 8p0q #1  
---  
UDP — uridine-5'-diphosphate  
  
8p0q mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> set bgColor white

> set bgColor #ffffff00

> open 8J30

Summary of feedback from opening 8J30 fetched from pdb  
---  
note | Fetching compressed mmCIF 8j30 from
http://files.rcsb.org/download/8j30.cif  
  
8j30 title:  
Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-
GLC [more info...]  
  
Chain information for 8j30 #2  
---  
Chain | Description | UniProt  
A B | UDP-glucose:protein N-beta-glucosyltransferase | NGT_ACTP2 1-620  
  
Non-standard residues in 8j30 #2  
---  
UDP — uridine-5'-diphosphate  
UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl-
monophosphate ester)  
  
8j30 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show "Selection Inspector"

> ui windowfill toggle

[Repeated 1 time(s)]

> open 8J30

8j30 title:  
Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-
GLC [more info...]  
  
Chain information for 8j30 #3  
---  
Chain | Description | UniProt  
A B | UDP-glucose:protein N-beta-glucosyltransferase | NGT_ACTP2 1-620  
  
Non-standard residues in 8j30 #3  
---  
UDP — uridine-5'-diphosphate  
UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl-
monophosphate ester)  
  
8j30 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #2

9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected  

> select #3

9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected  

> undo

[Repeated 1 time(s)]

> select #2

9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #2

> select #2:469,218

Nothing selected  

> select add #3

9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected  

> select add #1

19741 atoms, 20223 bonds, 3 pseudobonds, 2458 residues, 3 models selected  

> select subtract #1

9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #2:469

Nothing selected  

> select #3:469,218

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select #3:469,218 stick

Expected a keyword  

> style sel stick

Changed 20 atom styles  

> hide sel cartoons

> style sel stick

Changed 20 atom styles  

> select #3:469,218

20 atoms, 16 bonds, 4 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 20 atom styles  

> swapaa #3:469 gln 218 met

Expected a keyword  

> swapaa #3:469,218 gln,met

Using Dunbrack library  
8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/cmd.py", line 40, in swap_aa  
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa  
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers  
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params  
return self._get_params(res_name, file_name, cache, archive)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
  
See log for complete Python traceback.  
  

> swapaa #3:469,218 gln,met

Using Dunbrack library  
8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/cmd.py", line 40, in swap_aa  
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa  
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers  
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params  
return self._get_params(res_name, file_name, cache, archive)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
  
See log for complete Python traceback.  
  

> swapaa #3:469,218 seq:QM

Using Dunbrack library  
8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/cmd.py", line 40, in swap_aa  
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa  
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers  
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params  
return self._get_params(res_name, file_name, cache, archive)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A2000 12GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       2.7Gi        25Gi       298Mi       2.6Gi        27Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4680] (rev 0c)	
	Subsystem: Dell Device [1028:0a9f]	
	Kernel driver in use: i915

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
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    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Hi Samira,

Thanks for reporting this problem. It has been fixed in releases newer than the one you have, so if you upgrade to the current production release then things should work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab