KeyError saving mmCIF file

[xiangan.liu@…]

The following bug report has been submitted:
Platform:        Linux-5.8.0-59-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open wt-B10-a_sub2-C13.pdb

Chain information for wt-B10-a_sub2-C13.pdb  
---  
Chain | Description  
1.1/a 1.2/a 1.3/a 1.4/a 1.5/a 1.6/a 1.7/a 1.8/a 1.9/a 1.10/a 1.11/a 1.12/a
1.13/a | No description available  
  

> open /mnt/data/final2/adopted/fit/0-center/wt-c13/wt-B10-b_sub1-C13.pdb

Chain information for wt-B10-b_sub1-C13.pdb  
---  
Chain | Description  
2.1/b 2.2/b 2.3/b 2.4/b 2.5/b 2.6/b 2.7/b 2.8/b 2.9/b 2.10/b 2.11/b 2.12/b
2.13/b | No description available  
  

> select #1.1

87 atoms, 88 bonds, 11 residues, 1 model selected  

> select #1.2

87 atoms, 88 bonds, 11 residues, 1 model selected  

> select #1.3

87 atoms, 88 bonds, 11 residues, 1 model selected  

> select #1.4

87 atoms, 88 bonds, 11 residues, 1 model selected  

> select #1.5

87 atoms, 88 bonds, 11 residues, 1 model selected  

> select #1.1

87 atoms, 88 bonds, 11 residues, 1 model selected  

> color sel red

> select #2.1

87 atoms, 88 bonds, 11 residues, 1 model selected  

> color sel blue

> setattr #1.1/a chain chain_id a1

Assigning chain_id attribute to 1 item  

> setattr #1.1/a residue chain_id a1

Assigning chain_id attribute to 0 items  

> setattr #1.5/a chain chain_id a2

Assigning chain_id attribute to 1 item  

> setattr #1.6/a chain chain_id a3

Assigning chain_id attribute to 1 item  

> setattr #1.7/a chain chain_id a4

Assigning chain_id attribute to 1 item  

> setattr #1.8/a chain chain_id a5

Assigning chain_id attribute to 1 item  

> setattr #1.9/a chain chain_id a6

Assigning chain_id attribute to 1 item  

> setattr #1.10/a chain chain_id a7

Assigning chain_id attribute to 1 item  

> setattr #1.11/a chain chain_id a8

Assigning chain_id attribute to 1 item  

> setattr #1.12/a chain chain_id a9

Assigning chain_id attribute to 1 item  

> setattr #1.13/a chain chain_id a10

Assigning chain_id attribute to 1 item  

> setattr #1.2/a chain chain_id a11

Assigning chain_id attribute to 1 item  

> setattr #1.3/a chain chain_id a12

Assigning chain_id attribute to 1 item  

> setattr #1.4/a chain chain_id a13

Assigning chain_id attribute to 1 item  

> setattr #2.1/b chain chain_id b1

Assigning chain_id attribute to 1 item  

> setattr #2.5/b chain chain_id b2

Assigning chain_id attribute to 1 item  

> setattr #2.6/b chain chain_id b3

Assigning chain_id attribute to 1 item  

> setattr #2.7/b chain chain_id b4

Assigning chain_id attribute to 1 item  

> setattr #2.8/b chain chain_id b5

Assigning chain_id attribute to 1 item  

> setattr #2.9/b chain chain_id b6

Assigning chain_id attribute to 1 item  

> setattr #2.10/b chain chain_id b7

Assigning chain_id attribute to 1 item  

> setattr #2.11/b chain chain_id b8

Assigning chain_id attribute to 1 item  

> setattr #2.12/b chain chain_id b9

Assigning chain_id attribute to 1 item  

> setattr #2.13/b chain chain_id b10

Assigning chain_id attribute to 1 item  

> setattr #2.2/b chain chain_id b11

Assigning chain_id attribute to 1 item  

> setattr #2.3/b chain chain_id b12

Assigning chain_id attribute to 1 item  

> setattr #2.4/b chain chain_id b13

Assigning chain_id attribute to 1 item  

> select clear

> select clear

> save /mnt/data/final2/adopted/fit/0-center/wt-c13/wt-B10-a-b.cif

Not saving entity_poly_seq for non-authoritative sequences  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/mmcif/__init__.py", line 89, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 145, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 542, in
chimerax.mmcif.mmcif_write.save_structure  
KeyError: ('a1', 'RPGMMDSQEFS')  
  
KeyError: ('a1', 'RPGMMDSQEFS')  
  
File "src/mmcif_write.pyx", line 542, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/a1 #1.2/a11 #1.3/a12 #1.4/a13 #1.5/a2 #1.6/a3 #1.7/a4
> #1.8/a5 #1.9/a6 #1.10/a7 #1.11/a8 #1.12/a9 #1.13/a10 #2.1/b1 #2.2/b11
> #2.3/b12 #2.4/b13 #2.5/b2 #2.6/b3 #2.7/b4 #2.8/b5 #2.9/b6 #2.10/b7 #2.11/b8
> #2.12/b9 #2.13/b10

Alignment identifier is 1  

> save /mnt/data/final2/adopted/fit/0-center/wt-c13/wt-B10-a-b.cif

Not saving entity_poly_seq for non-authoritative sequences  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/mmcif/__init__.py", line 89, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 145, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 542, in
chimerax.mmcif.mmcif_write.save_structure  
KeyError: ('a1', 'RPGMMDSQEFS')  
  
KeyError: ('a1', 'RPGMMDSQEFS')  
  
File "src/mmcif_write.pyx", line 542, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.73.01
OpenGL renderer: Quadro P2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7820 Tower
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        35Gi       678Mi       164Mi        26Gi        26Gi
	Swap:         975Mi       589Mi       386Mi

Graphics:
	0000:b3:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106GL [Quadro P2200] [10de:1c31] (rev a1)	
	Subsystem: Dell GP106GL [Quadro P2200] [1028:131b]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
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    certifi: 2020.12.5
    cftime: 1.5.0
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    ChimeraX-AddCharge: 1.0.1
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    ChimeraX-AlignmentHdrs: 3.2
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    ChimeraX-CrystalContacts: 1.0
    ChimeraX-Cytoscape: 0.1
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    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
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    ChimeraX-Label: 1.0
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    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
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    ChimeraX-Mol2: 2.0
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    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
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    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.0.1
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    ChimeraX-Registration: 1.1
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    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.10
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
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    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StrudelScore: 0.1.4
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
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    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
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    wcwidth: 0.2.5
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    wheel: 0.36.0
    wheel-filename: 1.2.0

[Greg Couch]

Can you provide a ChimeraX session file with your modified PDB file that reproduces this error? That would help a lot.

[Greg Couch]

If you need to keep the data private, you can send it to me directly at gregc@….

[Greg Couch]

Okay, so I see that the PDB files are NMR ensembles. And then you changed the chain identifiers, which are supposed to be same in each NMR model. That confuses the code.

My guess is that you really want one model. If so, after opening the two PDB files, give the command:

combine #1,2 name wt-B10-a-b
save /mnt/data/final2/adopted/fit/0-center/wt-c13/wt-B10-a-b.cif model #3

Or some other name. That will automatically give you a different chain id for each chain.

[Greg Couch]

Eric, this is because after the setattr #1.1/a chain chain_id a1, chain.name != chain.chain_id in that structure. What is the semantic difference between the two?

[pett]

chain.name is almost never equal to chain.chain_id. chain.name is typically something like "chain A" whereas chain.chain_id is 'A'. Chain inherits name from Sequence, and is an arbitrary identifier used next to the sequence in alignments and in other textual contexts. By default, Structures assign the name "Chain chain_id" to their chains. If you are using a reasonably recent version of atomic_lib, the name is updated when the chain_id is changed (as long as it was still in the default form).

[Greg Couch]

Thanks.