Opened 15 months ago

Closed 15 months ago

#15821 closed defect (duplicate)

Save mmCIF: 'Residue' object has no attribute 'display'

Reported by: disha-gajanan.hiregange@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.14.0-427.20.1.el9_4.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/maps/rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc

Opened rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc as #1, grid
size 480,480,480, pixel 0.842, shown at level 0.0197, step 2, values float32  

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/new_merged_male_WT-
> coot-5.pdb

Chain information for new_merged_male_WT-coot-5.pdb #2  
---  
Chain | Description  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
Le | No description available  
Lf | No description available  
Lj | No description available  
S2 | No description available  
S6 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Se | No description available  
  

> vop all level 0.009

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule new_merged_male_WT-coot-5.pdb (#2) to map
rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc (#1) using 174882
atoms  
average map value = 0.01881, steps = 72  
shifted from previous position = 4.56  
rotated from previous position = 1.11 degrees  
atoms outside contour = 13734, contour level = 0.009  
  
Position of new_merged_male_WT-coot-5.pdb (#2) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99983902 0.01792169 0.00086617 -5.11975234  
-0.01792739 0.99981412 0.00709474 -0.10667676  
-0.00073886 -0.00710912 0.99997446 5.40176026  
Axis -0.36803470 0.04158777 -0.92888154  
Axis point -2.30140102 350.08958166 0.00000000  
Rotation angle (degrees) 1.10569970  
Shift along axis -3.13778531  
  

> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/new_merged_male_WT-
> coot-5.pdb relModel #1

> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/new_merged_male_WT_class3.cif
> relModel #2

Not saving entity_poly_seq for non-authoritative sequences  

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class1/phenix/RealSpaceRefine_4/RPS9_FMT_class1_real_space_refined_004.cif

Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class1/phenix/RealSpaceRefine_4/RPS9_FMT_class1_real_space_refined_004.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 5897  
Missing entity information. Treating each chain as a separate entity.  
Invalid residue range for struct_conf "1": invalid chain "LO", near line 175  
Invalid residue range for struct_conf "2": invalid chain "LO", near line 176  
Invalid residue range for struct_conf "3": invalid chain "LO", near line 177  
Invalid residue range for struct_conf "4": invalid chain "LO", near line 178  
Invalid residue range for struct_conf "5": invalid chain "LO", near line 179  
261 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "1 1": invalid chain "LO", near
line 5720  
Invalid sheet range for struct_sheet_range "2 1": invalid chain "LO", near
line 5721  
Invalid sheet range for struct_sheet_range "3 1": invalid chain "LO", near
line 5722  
Invalid sheet range for struct_sheet_range "4 1": invalid chain "LO", near
line 5723  
Invalid sheet range for struct_sheet_range "5 1": invalid chain "LO", near
line 5724  
171 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 175137  
Skipping chem_comp category: Missing column 'type' near line 175422  
Skipping chem_comp category: Missing column 'type' near line 175701  
Skipping chem_comp category: Missing column 'type' near line 175962  
Skipping chem_comp category: Missing column 'type' near line 176214  
6 messages similar to the above omitted  
  
Chain information for RPS9_FMT_class1_real_space_refined_004.cif #3  
---  
Chain | Description  
At | No description available  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
Le | No description available  
Lf | No description available  
Lj | No description available  
Pt | No description available  
S2 | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SI | No description available  
SJ | No description available  
SL | No description available  
SO | No description available  
SP | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SZ | No description available  
Sb | No description available  
Se | No description available  
mR | No description available  
  

> ui tool show Matchmaker

> matchmaker #!3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker new_merged_male_WT-coot-5.pdb, chain L5 (#2) with
RPS9_FMT_class1_real_space_refined_004.cif, chain L5 (#3), sequence alignment
score = 21009.3  
RMSD between 3408 pruned atom pairs is 0.639 angstroms; (across all 3471
pairs: 0.733)  
  

> fitmap #3 inMap #1

Fit molecule RPS9_FMT_class1_real_space_refined_004.cif (#3) to map
rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc (#1) using 169161
atoms  
average map value = 0.01775, steps = 108  
shifted from previous position = 0.246  
rotated from previous position = 0.0818 degrees  
atoms outside contour = 24815, contour level = 0.009  
  
Position of RPS9_FMT_class1_real_space_refined_004.cif (#3) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class3_with_blush.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74152892 -0.53802422 0.40083013 373.48316616  
0.28925938 -0.79542972 -0.53256039 421.30495510  
0.60536259 -0.27896506 0.74546270 -28.46437144  
Axis 0.28521917 -0.23003805 0.93044748  
Axis point 138.50183157 254.80570625 0.00000000  
Rotation angle (degrees) 153.60466679  
Shift along axis -16.87621621  
  

> hide #!2 models

> close session

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class1/run_class001.mrc

Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00708, step 2, values float32  

> vop all level 0.009

> vop all level 0.003

> surface dust #1 size 8.19

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class2/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.819, shown at
level 0.00697, step 2, values float32  

> hide #!1 models

> vop all level 0.003

> vop all level 0.002

> surface dust #2 size 8.19

> show #!1 models

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit map run_class001.mrc in map run_class001.mrc using 775091 points  
correlation = 0.8124, correlation about mean = 0.7271, overlap = 16.52  
steps = 92, shift = 0.628, angle = 2.51 degrees  
  
Position of run_class001.mrc (#1) relative to run_class001.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99907727 -0.03765804 -0.02065158 11.67379123  
0.03748808 0.99926044 -0.00855610 -6.17018865  
0.02095851 0.00777402 0.99975012 -5.76386414  
Axis 0.18676707 -0.47589334 0.85944377  
Axis point 168.54063480 305.05694482 0.00000000  
Rotation angle (degrees) 2.50564866  
Shift along axis 0.16291431  
  

> close session

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady-
> coot.cif-coot-1.pdb

Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady-
coot.cif-coot-1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE P 26
THR P 32 1 7  
Start residue of secondary structure not found: HELIX 2 2 ALA P 33 ALA P 35 1
3  
Start residue of secondary structure not found: HELIX 3 3 ILE P 41 VAL P 51 1
11  
Start residue of secondary structure not found: HELIX 4 4 LYS P 74 TRP P 76 1
3  
Start residue of secondary structure not found: HELIX 5 5 LYS P 85 GLU P 103 1
19  
84 messages similar to the above omitted  
note | Combining 56 symmetry atoms into VAL /LO:203  
  
Chain information for
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady-
coot.cif-coot-1.pdb #1  
---  
Chain | Description  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
Le | No description available  
Lf | No description available  
Lj | No description available  
S2 | No description available  
S6 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Se | No description available  
  
Drag select of 1 atoms  

> hide sel atoms

> hide sel cartoons

> select clear

Drag select of 30 atoms  

> hide sel atoms

> hide sel cartoons

> select clear

> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady_corrected.cif
> displayedOnly true relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 123, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 160, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 167, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure  
AttributeError: 'Residue' object has no attribute 'display'  
  
AttributeError: 'Residue' object has no attribute 'display'  
  
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 550.90.07
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=plasmax11
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.4 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        51Gi       6.6Gi       253Mi       5.4Gi        10Gi
	Swap:           31Gi       6.0Gi        25Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Save mmCIF: 'Residue' object has no attribute 'display'

comment:2 by Eric Pettersen, 15 months ago

Resolution: → duplicate
Status: assigned → closed

Hi Disha,

Thanks for reporting this problem. It is fixed in the ChimeraX 1.8 release, so if you get that then you won't run into this anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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