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Opened 24 hours ago
Closed 8 hours ago
#20553 closed defect (duplicate)
Session save: 'BlastProteinResults' object has no attribute 'table'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.12rc202605080108 (2026-05-08 01:08:27 UTC)
Description
can't save session
Log:
UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/aleezamughal/Desktop/WbdP comparison + other
> glycosyltransferases.cxs" format session
Populating font family aliases took 122 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
Log from Thu Jun 11 09:46:05 2026You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2026-06-07 10:27:40,162 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("HTTPConnection(host='webservices.rbvi.ucsf.edu',
port=80): Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8] nodename
nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=26bda3e7-294b-5ab6-b4f3-7855aee7c14c&OS=macosx&Arch=arm64&OSVersion=26.2&ChimeraXVersion=1.12rc202605080108
2026-06-07 10:27:40,164 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("HTTPConnection(host='webservices.rbvi.ucsf.edu',
port=80): Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8] nodename
nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=26bda3e7-294b-5ab6-b4f3-7855aee7c14c&OS=macosx&Arch=arm64&OSVersion=26.2&ChimeraXVersion=1.12rc202605080108
2026-06-07 10:27:40,180 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("HTTPConnection(host='webservices.rbvi.ucsf.edu',
port=80): Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8] nodename
nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=26bda3e7-294b-5ab6-b4f3-7855aee7c14c&OS=macosx&Arch=arm64&OSVersion=26.2&ChimeraXVersion=1.12rc202605080108
> open A0A9Q6ZED9 format mmcif fromDatabase alphafold
Summary of feedback from opening A0A9Q6ZED9 fetched from alphafold
---
note | Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Chain information for AlphaFold A0A9Q6ZED9 #1
---
Chain | Description | UniProt
A | Glycosyl transferase | A0A9Q6ZED9_ECO57 1-404
Color AlphaFold A0A9Q6ZED9 by residue attribute pLDDT_score
> open
> /Users/aleezamughal/Downloads/fold_2026_05_15_15_51/fold_2026_05_15_15_51_model_0.cif
> format mmcif
Chain information for fold_2026_05_15_15_51_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> hide #2 models
> show #2 models
> open
> /Users/aleezamughal/Downloads/fold_2026_05_15_15_51/fold_2026_05_15_15_51_model_1.cif
> format mmcif
Chain information for fold_2026_05_15_15_51_model_1.cif #3
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/aleezamughal/Downloads/fold_2026_05_15_15_51
> 2/fold_2026_05_15_15_51_model_2.cif" format mmcif
Chain information for fold_2026_05_15_15_51_model_2.cif #4
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/aleezamughal/Downloads/fold_2026_05_15_15_51
> 2/fold_2026_05_15_15_51_model_3.cif" format mmcif
Chain information for fold_2026_05_15_15_51_model_3.cif #5
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/aleezamughal/Downloads/fold_2026_05_15_15_51
> 2/fold_2026_05_15_15_51_model_4.cif" format mmcif
Chain information for fold_2026_05_15_15_51_model_4.cif #6
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_2026_06_01_00_39/fold_2026_06_01_00_39_model_0.cif
> format mmcif
Chain information for fold_2026_06_01_00_39_model_0.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_2026_06_01_00_39/fold_2026_06_01_00_39_model_1.cif
> format mmcif
Chain information for fold_2026_06_01_00_39_model_1.cif #8
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_2026_06_01_00_39/fold_2026_06_01_00_39_model_2.cif
> format mmcif
Chain information for fold_2026_06_01_00_39_model_2.cif #9
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_2026_06_01_00_39/fold_2026_06_01_00_39_model_3.cif
> format mmcif
Chain information for fold_2026_06_01_00_39_model_3.cif #10
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_2026_06_01_00_39/fold_2026_06_01_00_39_model_4.cif
> format mmcif
Chain information for fold_2026_06_01_00_39_model_4.cif #11
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-11 to #1
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 AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_0.cif, chain A (#2), sequence alignment score =
2101.2
RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
2.582)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_1.cif, chain A (#3), sequence alignment score =
2083.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_1.cif #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 351 pruned atom pairs is 0.790 angstroms; (across all 404 pairs:
2.779)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_2.cif, chain A (#4), sequence alignment score =
2110.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_2.cif #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 374 pruned atom pairs is 0.723 angstroms; (across all 404 pairs:
1.327)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_3.cif, chain A (#5), sequence alignment score =
2121.6
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_3.cif #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 367 pruned atom pairs is 0.649 angstroms; (across all 404 pairs:
2.750)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_4.cif, chain A (#6), sequence alignment score =
2083.8
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_4.cif #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 365 pruned atom pairs is 0.658 angstroms; (across all 404 pairs:
1.919)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_0.cif, chain A (#7), sequence alignment score =
2110.8
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_0.cif #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 371 pruned atom pairs is 0.326 angstroms; (across all 404 pairs:
1.148)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_1.cif, chain A (#8), sequence alignment score =
2102.4
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_1.cif #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 372 pruned atom pairs is 0.349 angstroms; (across all 404 pairs:
1.533)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_2.cif, chain A (#9), sequence alignment score =
2115
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_2.cif #9/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 374 pruned atom pairs is 0.420 angstroms; (across all 404 pairs:
2.359)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_3.cif, chain A (#10), sequence alignment score =
2117.4
Alignment identifier is 8
Showing conservation header ("seq_conservation" residue attribute) for
alignment 8
Hiding conservation header for alignment 8
Chains used in RMSD evaluation for alignment 8: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_3.cif #10/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 8
RMSD between 370 pruned atom pairs is 0.363 angstroms; (across all 404 pairs:
1.682)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_4.cif, chain A (#11), sequence alignment score =
2098.8
Alignment identifier is 9
Showing conservation header ("seq_conservation" residue attribute) for
alignment 9
Hiding conservation header for alignment 9
Chains used in RMSD evaluation for alignment 9: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_4.cif #11/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 9
RMSD between 373 pruned atom pairs is 0.398 angstroms; (across all 404 pairs:
1.169)
> show #7 target m
> undo
> open A0A9Q6ZED9 format mmcif fromDatabase alphafold
Chain information for AlphaFold A0A9Q6ZED9 #12
---
Chain | Description | UniProt
A | Glycosyl transferase | A0A9Q6ZED9_ECO57 1-404
Color AlphaFold A0A9Q6ZED9 by residue attribute pLDDT_score
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_05_15_15_51_model_1.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_1.cif #3/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 2: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_2.cif #4/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 3: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_3.cif #5/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 4: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_05_15_15_51_model_4.cif #6/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 5: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_0.cif #7/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 6: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_1.cif #8/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 7: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_2.cif #9/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 8: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_3.cif #10/A, AlphaFold A0A9Q6ZED9 #12/A
Associated AlphaFold A0A9Q6ZED9 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 9: AlphaFold A0A9Q6ZED9 #1/A,
fold_2026_06_01_00_39_model_4.cif #11/A, AlphaFold A0A9Q6ZED9 #12/A
> hide #12 models
> show #12 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #2 models
> ui mousemode right zoom
> ui tool show "Blast Protein"
> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1
Webservices job id: HXB6NR4VOTTJAXK8
Webservices job finished: HXB6NR4VOTTJAXK8
BLAST search returned no results.
> hide #2 models
> ui tool show "Blast Protein"
> blastprotein #1/A database alphafold cutoff 1e-4 matrix BLOSUM62 maxSeqs 100
> version 4 name bp2
Webservices job id: ML1SQMO3YCCAI7RO
> hide #7 models
> ui tool show "Blast Protein"
> show #1 models
> blastprotein #1/A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp3
Webservices job id: WBX83DJWPCQOFJFM
> blastprotein #1/A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp4
Webservices job id: O0DODQD55IYQK1DS
Webservices job finished: ML1SQMO3YCCAI7RO
> alphafold fetch A0A4B9BQ02 version 4 alignTo #1/A
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch A0A4B9BQ02 version 4 alignTo #1/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Blast Protein"
> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp5
Webservices job id: EE5M82Q3W5Z6Y7PJ
Webservices job finished: EE5M82Q3W5Z6Y7PJ
BLAST search returned no results.
> ui tool show "Blast Protein"
> blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp6
Webservices job id: RJFJ37L2H7BDKLC1
Webservices job finished: RJFJ37L2H7BDKLC1
BLAST search returned no results.
> ui tool show "Blast Protein"
> undo
> redo
> ui tool show "Blast Protein"
> blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp7
Webservices job id: S3S036356GY25XCQ
Webservices job finished: S3S036356GY25XCQ
BLAST search returned no results.
Exception in thread Thread-135 (_run_function):
Traceback (most recent call last):
Exception in thread Thread-123 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 204, in _new_conn
[Repeated 1 time(s)] sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 60, in create_connection
sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 60, in create_connection
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for res in socket.getaddrinfo(host,
port, family, socket.SOCK_STREAM):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 962, in getaddrinfo
[Repeated 1 time(s)] for res in _socket.getaddrinfo(host, port, family, type,
proto, flags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 788, in urlopen
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 788, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 493, in _make_request
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 493, in _make_request
conn.request(
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 500, in request
conn.request(
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 500, in request
self.endheaders()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1298, in endheaders
self.endheaders()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1058, in _send_output
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1058, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 996, in send
self.send(msg)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 996, in send
self.connect()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 331, in connect
self.connect()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 331, in connect
self.sock = self._new_conn()
^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 211, in _new_conn
self.sock = self._new_conn()
^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 211, in _new_conn
raise NameResolutionError(self.host, self, e) from e
urllib3.exceptions.NameResolutionError:
HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80): Failed to resolve
'webservices.rbvi.ucsf.edu' ([Errno 8] nodename nor servname provided, or not
known)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1045, in _bootstrap_inner
raise NameResolutionError(self.host, self, e) from e
urllib3.exceptions.NameResolutionError:
HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80): Failed to resolve
'webservices.rbvi.ucsf.edu' ([Errno 8] nodename nor servname provided, or not
known)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1045, in _bootstrap_inner
self.run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 982, in run
self.run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 982, in run
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 323, in _run_function
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 323, in _run_function
func(*args, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 172, in run
func(*args, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 172, in run
super().run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 486, in run
super().run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 486, in run
self.monitor()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 207, in monitor
self.monitor()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 207, in monitor
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 1013, in
get_status_with_http_info
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 1013, in
get_status_with_http_info
return self.api_client.call_api(
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.api_client.call_api(
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 151, in __call_api
return self.__call_api(resource_path, method,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 341, in request
response_data = self.request(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 228, in GET
return self.rest_client.GET(url,
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 228, in GET
return self.request("GET", url,
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 206, in request
return self.request("GET", url,
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 206, in request
r = self.pool_manager.request(method, url,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 135, in request
return self.request_encode_url(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 182, in request_encode_url
r = self.pool_manager.request(method, url,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 135, in request
return self.urlopen(method, url, **extra_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/poolmanager.py", line 457, in urlopen
return self.request_encode_url(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 182, in request_encode_url
return self.urlopen(method, url, **extra_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/poolmanager.py", line 457, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 842, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 842, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/retry.py", line 543, in increment
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/retry.py", line 543, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url: /cxservices/api/v1/chimerax/jobs/WBX83DJWPCQOFJFM/status
(Caused by
NameResolutionError("HTTPConnection(host='webservices.rbvi.ucsf.edu',
port=80): Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8] nodename
nor servname provided, or not known)"))
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url: /cxservices/api/v1/chimerax/jobs/O0DODQD55IYQK1DS/status
(Caused by
NameResolutionError("HTTPConnection(host='webservices.rbvi.ucsf.edu',
port=80): Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8] nodename
nor servname provided, or not known)"))
> ui tool show "Blast Protein"
> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp8
Webservices job id: AUPIY0P8FRGSAYZN
Webservices job finished: AUPIY0P8FRGSAYZN
BLAST search returned no results.
> ui tool show "Blast Protein"
> blastprotein #1/A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp9
Webservices job id: 4W12WWU66IE25Z42
> ui tool show "Blast Protein"
> blastprotein A0A9Q6ZED9 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp10
Webservices job id: 2GQKQ10EIBRUXHJR
Webservices job finished: 2GQKQ10EIBRUXHJR
BLAST search returned no results.
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> select #1/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> select #1/A:404
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> open AADWCW010000115.1
Unrecognized file suffix '.1'
> open AADWCW010000115
'AADWCW010000115' has no suffix
> open accession AADWCW010000115
'accession' has no suffix
> open genbank AADWCW010000115.1
'genbank' has no suffix
> open genbank AADWCW010000115
'genbank' has no suffix
> open genbank AADWCW010000000
'genbank' has no suffix
> open GenBank AADWCW010000000
'GenBank' has no suffix
> open GenBank AADWCW010000000.1
'GenBank' has no suffix
> open /Users/aleezamughal/Downloads/sequence.fasta
Summary of feedback from opening /Users/aleezamughal/Downloads/sequence.fasta
---
note | Alignment identifier is sequence.fasta
Opened 1 sequence from sequence.fasta
> open "/Users/aleezamughal/Downloads/salmonella enterica.fasta"
Summary of feedback from opening /Users/aleezamughal/Downloads/salmonella
enterica.fasta
---
note | Alignment identifier is salmonella enterica.fasta
Opened 1 sequence from salmonella enterica.fasta
> ui tool show ViewDock
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.4.6 which is incompatible.
scipy 1.14.0 requires numpy<2.3,>=1.23.5, but you have numpy 2.4.6 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder #1
7 cavities found for AlphaFold A0A9Q6ZED9 #1
AlphaFold A0A9Q6ZED9 Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.1 | | 3694.25 | 2167.29 | 17103 | 9.37 | 2.92
1.1.5 | | 103.03 | 107.56 | 477 | 4.2 | 1.37
1.1.2 | | 94.18 | 104.19 | 436 | 4.84 | 1.66
1.1.6 | | 42.12 | 60.02 | 195 | 2.4 | 0.73
1.1.3 | | 37.15 | 51.03 | 172 | 1.9 | 0.46
1.1.4 | | 26.14 | 35.02 | 121 | 1.9 | 0.63
1.1.7 | | 12.31 | 29.54 | 57 | 0 | 0
Populating font family aliases took 161 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> undo
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> undo
> ui tool show "Side View"
> ui tool show "Blast Protein"
> blastprotein #12/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
> 100 version 4 name bp11
Webservices job id: F4Y99P2AEFHN9LAT
> show #2 models
> hide #2 models
> ui tool show "Blast Protein"
> blastprotein #!1/A database uniref100 cutoff 1e-3 matrix BLOSUM62 maxSeqs
> 100 version 1 name bp12
Webservices job id: N4DO18Q64JR60M21
> hide #!1.1 models
Webservices job finished: F4Y99P2AEFHN9LAT
> alphafold fetch A0A2W4UJ55 version 4 alignTo #12/A
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Fetching compressed AlphaFold A0A2W4UJ55 from
https://alphafold.ebi.ac.uk/files/AF-A0A2W4UJ55-F1-model_v6.cif
AlphaFold prediction matching chain A
---
Chain| UniProt Id| RMSD| Length| Seen| % Id
A | A0A2W4UJ55 | 10.54 | 392 | 404 | 27
> matchmaker #13 to #12/A
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 AlphaFold A0A9Q6ZED9, chain A (#12) with AlphaFold A0A2W4UJ55,
chain A (#13), sequence alignment score = 661.2
RMSD between 180 pruned atom pairs is 1.086 angstroms; (across all 383 pairs:
10.536)
Alignment identifier is bp11 [1]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated AlphaFold A0A2W4UJ55 chain A to A0A2W4UJ55 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [1]
> ui tool show Matchmaker
> matchmaker #12-13 to #1
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 AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A9Q6ZED9, chain
A (#12), sequence alignment score = 2144.4
RMSD between 404 pruned atom pairs is 0.000 angstroms; (across all 404 pairs:
0.000)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A2W4UJ55, chain
A (#13), sequence alignment score = 661.2
RMSD between 180 pruned atom pairs is 1.086 angstroms; (across all 383 pairs:
10.536)
> show #12 models
> hide #12 models
> hide #!1 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> hide #13 models
> show #12 models
Alignment identifier is bp11 [2]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [2]
Alignment identifier is bp11 [3]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [3]
Exception in thread Thread-288 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 204, in _new_conn
sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 85, in create_connection
raise err
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
OSError: [Errno 65] No route to host
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 788, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 493, in _make_request
conn.request(
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 500, in request
self.endheaders()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1058, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 996, in send
self.connect()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 331, in connect
self.sock = self._new_conn()
^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 219, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError:
HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80): Failed to establish
a new connection: [Errno 65] No route to host
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1045, in _bootstrap_inner
self.run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 982, in run
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 323, in _run_function
func(*args, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 172, in run
super().run()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 486, in run
self.monitor()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 207, in monitor
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 1013, in
get_status_with_http_info
return self.api_client.call_api(
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 228, in GET
return self.request("GET", url,
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/rest.py", line 206, in request
r = self.pool_manager.request(method, url,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 135, in request
return self.request_encode_url(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/_request_methods.py", line 182, in request_encode_url
return self.urlopen(method, url, **extra_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/poolmanager.py", line 457, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 872, in urlopen
return self.urlopen(
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 842, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/retry.py", line 543, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url: /cxservices/api/v1/chimerax/jobs/N4DO18Q64JR60M21/status
(Caused by
NewConnectionError("HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80):
Failed to establish a new connection: [Errno 65] No route to host"))
Alignment identifier is bp11 [4]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [4]
Alignment identifier is bp11 [5]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [5]
Alignment identifier is bp11 [6]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [6]
Alignment identifier is bp11 [7]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [7]
Alignment identifier is bp11 [8]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [8]
Alignment identifier is bp11 [9]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [9]
Alignment identifier is bp11 [10]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [10]
Alignment identifier is bp11 [11]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [11]
Alignment identifier is bp11 [12]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [12]
Alignment identifier is bp11 [13]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [13]
Alignment identifier is bp11 [14]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [14]
Alignment identifier is bp11 [15]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [15]
Alignment identifier is bp11 [16]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [16]
Alignment identifier is bp11 [17]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [17]
Alignment identifier is bp11 [18]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [18]
Alignment identifier is bp11 [19]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [19]
Alignment identifier is bp11 [20]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [20]
Alignment identifier is bp11 [21]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [21]
Alignment identifier is bp11 [22]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [22]
Alignment identifier is bp11 [23]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [23]
Alignment identifier is bp11 [24]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [24]
Alignment identifier is bp11 [25]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [25]
Alignment identifier is bp11 [26]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [26]
Alignment identifier is bp11 [27]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [27]
Alignment identifier is bp11 [28]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [28]
Alignment identifier is bp11 [29]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [29]
Alignment identifier is bp11 [30]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [30]
Alignment identifier is bp11 [31]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [31]
Alignment identifier is bp11 [32]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [32]
Alignment identifier is bp11 [33]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [33]
> alphafold fetch R6HU74 version 4 alignTo #12/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch R6HU74 version 4 alignTo #12/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch B5EGV0 version 4 alignTo #12/A
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 404, in <lambda>
seq_action.triggered.connect(lambda: self.load(self.table.selected))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 555, in load
models, chain_id = db.load_model(
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/data_model/databases.py", line 289, in
load_model
models, _ = run(chimerax_session, cmd)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/fetch.py", line 50, in alphafold_fetch
filename = fetch_file(session, url, 'AlphaFold %s' % uniprot_id, file_name,
'AlphaFold',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/fetch.py", line 99, in fetch_file
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/fetch.py", line 192, in retrieve_url
with urlopen(request, timeout=timeout, context=ssl_context) as response:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1352, in do_open
r = h.getresponse()
^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1395, in getresponse
response.begin()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 325, in begin
version, status, reason = self._read_status()
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 294, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
http.client.RemoteDisconnected: Remote end closed connection without response
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 294, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
See log for complete Python traceback.
> alphafold fetch R6HU74 version 4 alignTo #12/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
failed:
<urlopen error [Errno 8] nodename nor servname provided, or not known>
Alignment identifier is bp11 [34]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [34]
Alignment identifier is bp11 [35]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [35]
Alignment identifier is bp11 [36]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [36]
Alignment identifier is bp11 [37]
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #12/A with 0
mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #12/A with 0
mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #12/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp11 [37]
> alphafold fetch A0A4R7CL53 version 4 alignTo #12/A
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4R7CL53-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> show #13 models
> hide #13 models
> save "/Users/aleezamughal/Desktop/WbdP comparison + other
> glycosyltransferases.cxs"
——— End of log from Thu Jun 11 09:46:05 2026 ———
> view name session-start
opened ChimeraX session
BLAST job failed
[Repeated 3 time(s)]
> show #!1 models
> hide #12 models
> show #11 models
> hide #11 models
> show #2 models
> hide #!1 models
> show #7 models
> show #3 models
> hide #3 models
> hide #2 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select
> #7/A:14-29,44-63,78-86,101-110,125-129,140-142,145-147,150-165,175-184,203-206,210-212,214-216,231-233,235-247,268-278,282-284,293-302,318-326,339-341,355-367,374-403
1620 atoms, 1635 bonds, 197 residues, 1 model selected
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select
> #7/A:14-29,44-63,78-86,101-110,125-129,140-142,145-147,150-165,175-184,203-206,210-212,214-216,231-233,235-247,268-278,282-284,293-302,318-326,339-341,355-367,374-403
1620 atoms, 1635 bonds, 197 residues, 1 model selected
> select
> #7/A:2-6,34-40,93-97,115-117,169-172,191-194,222-226,253-257,285-289,306-308,331-334,347-350
436 atoms, 433 bonds, 54 residues, 1 model selected
> select ::name="TYR"
3372 atoms, 3397 bonds, 281 residues, 13 models selected
> show (#7 & sel-residues & sidechain) target ab
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> show #2 models
> hide #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Sequence Viewer"
> select ::name="TYR"
3372 atoms, 3397 bonds, 281 residues, 13 models selected
> show (#2 & sel-residues & sidechain) target ab
> select #2/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #7 models
> hide #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:245-246
23 atoms, 23 bonds, 2 residues, 1 model selected
> select #7/A:245-246
23 atoms, 23 bonds, 2 residues, 1 model selected
> select
> #7/A:14-29,44-63,78-86,101-110,125-129,140-142,145-147,150-165,175-184,203-206,210-212,214-216,231-233,235-247,268-278,282-284,293-302,318-326,339-341,355-367,374-403
1620 atoms, 1635 bonds, 197 residues, 1 model selected
> select #7/A:195-196
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #7/A:195-198
32 atoms, 33 bonds, 4 residues, 1 model selected
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #7/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #7 models
> show #2 models
> hide #2 models
> show #7 models
> select ::name="GDP"
140 atoms, 150 bonds, 5 residues, 5 models selected
> undo
> redo
> show #2 models
> show #11 models
> show #10 models
> hide #10 models
> hide #11 models
> hide #7 models
> hide #2 models
> show #7 models
> hide #7 models
> show #2 models
> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_0.cif
Chain information for fold_gdp_bound_wbdp_model_0.cif #14
---
Chain | Description
A | .
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-14 to #1
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 AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_0.cif, chain A (#2), sequence alignment score =
2101.2
RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
2.582)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_1.cif, chain A (#3), sequence alignment score =
2083.8
Alignment identifier is 10
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10
Hiding conservation header for alignment 10
Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_1.cif #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10
RMSD between 351 pruned atom pairs is 0.790 angstroms; (across all 404 pairs:
2.779)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_2.cif, chain A (#4), sequence alignment score =
2110.2
Alignment identifier is 11
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11
Hiding conservation header for alignment 11
Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11
RMSD between 374 pruned atom pairs is 0.723 angstroms; (across all 404 pairs:
1.327)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_3.cif, chain A (#5), sequence alignment score =
2121.6
Alignment identifier is 12
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12
Hiding conservation header for alignment 12
Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12
RMSD between 367 pruned atom pairs is 0.649 angstroms; (across all 404 pairs:
2.750)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_4.cif, chain A (#6), sequence alignment score =
2083.8
Alignment identifier is 13
Showing conservation header ("seq_conservation" residue attribute) for
alignment 13
Hiding conservation header for alignment 13
Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 13
RMSD between 365 pruned atom pairs is 0.658 angstroms; (across all 404 pairs:
1.919)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_0.cif, chain A (#7), sequence alignment score =
2110.8
Alignment identifier is 14
Showing conservation header ("seq_conservation" residue attribute) for
alignment 14
Hiding conservation header for alignment 14
Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 14
RMSD between 371 pruned atom pairs is 0.326 angstroms; (across all 404 pairs:
1.148)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_1.cif, chain A (#8), sequence alignment score =
2102.4
Alignment identifier is 15
Showing conservation header ("seq_conservation" residue attribute) for
alignment 15
Hiding conservation header for alignment 15
Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 15
RMSD between 372 pruned atom pairs is 0.349 angstroms; (across all 404 pairs:
1.533)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_2.cif, chain A (#9), sequence alignment score =
2115
Alignment identifier is 16
Showing conservation header ("seq_conservation" residue attribute) for
alignment 16
Hiding conservation header for alignment 16
Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 16
RMSD between 374 pruned atom pairs is 0.420 angstroms; (across all 404 pairs:
2.359)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_3.cif, chain A (#10), sequence alignment score =
2117.4
Alignment identifier is 17
Showing conservation header ("seq_conservation" residue attribute) for
alignment 17
Hiding conservation header for alignment 17
Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 17
RMSD between 370 pruned atom pairs is 0.363 angstroms; (across all 404 pairs:
1.682)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_06_01_00_39_model_4.cif, chain A (#11), sequence alignment score =
2098.8
Alignment identifier is 18
Showing conservation header ("seq_conservation" residue attribute) for
alignment 18
Hiding conservation header for alignment 18
Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 18
RMSD between 373 pruned atom pairs is 0.398 angstroms; (across all 404 pairs:
1.169)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A9Q6ZED9, chain
A (#12), sequence alignment score = 2144.4
Alignment identifier is 19
Showing conservation header ("seq_conservation" residue attribute) for
alignment 19
Hiding conservation header for alignment 19
Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 19
RMSD between 404 pruned atom pairs is 0.000 angstroms; (across all 404 pairs:
0.000)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A2W4UJ55, chain
A (#13), sequence alignment score = 661.2
RMSD between 180 pruned atom pairs is 1.086 angstroms; (across all 383 pairs:
10.536)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_gdp_bound_wbdp_model_0.cif, chain A (#14), sequence alignment score =
2105.4
Alignment identifier is 20
Showing conservation header ("seq_conservation" residue attribute) for
alignment 20
Hiding conservation header for alignment 20
Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 20
RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
1.657)
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> hide #2 models
> select ::name="TYR"
3648 atoms, 3675 bonds, 304 residues, 14 models selected
> show (#14 & sel-residues & sidechain) target ab
> select #2/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:245
16 atoms, 16 bonds, 1 residue, 1 model selected
> undo
[Repeated 2 time(s)]
> redo
> show #2 models
> select ::name="TYR"
3648 atoms, 3675 bonds, 304 residues, 14 models selected
> select ::name="TYR"
3648 atoms, 3675 bonds, 304 residues, 14 models selected
> color (#2,14 & sel) hot pink
> undo
> redo
> undo
> select #2/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:8-9
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right zoom
> ui tool show H-Bonds
> hbonds reveal true
64593 hydrogen bonds found
> hide #2 models
> show #2 models
> hide #2 models
> undo
[Repeated 2 time(s)]
> redo
> hide #2 models
> ui tool show H-Bonds
> hbonds delete
> show #2 models
> hide #2 models
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
4 hydrogen bonds found
> ui tool show "Show Sequence Viewer"
> sequence chain #14/A
Alignment identifier is 14/A
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
4 hydrogen bonds found
> select #14/A:306
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:306-326
144 atoms, 147 bonds, 21 residues, 1 model selected
> hide #14 models
> show #14 models
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
28 hydrogen bonds found
> select #14/A:327
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A:327-337
83 atoms, 82 bonds, 11 residues, 1 model selected
> select #14/A:12
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/A:12-22
91 atoms, 94 bonds, 11 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
16 hydrogen bonds found
> select #14/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A
3292 atoms, 3376 bonds, 16 pseudobonds, 404 residues, 2 models selected
> select #14/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #14/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> hide #14.1 models
> select ::name="GDP"
168 atoms, 180 bonds, 6 residues, 6 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
53 hydrogen bonds found
> show #14.1 models
> show #!2 models
> select ::name="GDP"
168 atoms, 180 bonds, 6 residues, 6 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true
53 hydrogen bonds found
> hide #!14 models
> hide #14.1 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> color #2.1 #fa86eeff models
> hide #2.1 models
> hide #!2 models
> show #!14 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!2 models
> show #2.1 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #14.1 models
> hide #14.1 models
> show #14.1 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #14.1 models
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence.
[Repeated 1 time(s)]
> show #!1 models
Cannot run BLAST without some kind of sequence.
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence.
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence.
> ui tool show "Show Sequence Viewer"
> sequence chain #!1/A
Alignment identifier is 1/A
> select #!1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #!1/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
Cannot run BLAST without some kind of sequence.
> blastprotein #!1/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
> 100 version 4 name bp2
Webservices job id: 8FGDOPM8NPCA8EN8
> select #14/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> select #14/A:305
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #14/A:303-305
19 atoms, 18 bonds, 3 residues, 1 model selected
Webservices job finished: 8FGDOPM8NPCA8EN8
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 937, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/job.py", line 132, in on_finish
BlastProteinResults.from_job(
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 118, in from_job
return cls(session, tool_name, from_restore=False, params=params, job=job,
**kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 100, in __init__
self._build_ui()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 262, in _build_ui
param_str = self._format_param_str()
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 222, in _format_param_str
model_no = int(float(values[0].split("/")[0][1:]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: could not convert string to float: '!1'
ValueError: could not convert string to float: '!1'
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 222, in _format_param_str
model_no = int(float(values[0].split("/")[0][1:]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select
> #14/A:14-29,44-63,78-85,101-110,127-129,140-143,145-147,150-165,175-184,203-206,210-212,214-216,231-233,235-247,268-279,282-284,293-301,318-326,339-341,355-367,374-403
1609 atoms, 1625 bonds, 195 residues, 1 model selected
> select #14/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> select #14/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #14/A
3292 atoms, 3376 bonds, 404 residues, 1 model selected
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence.
> blastprotein #!1/A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp3
Webservices job id: FYN32J0BLRKN59QN
> ui tool show ViewDock
> hide #!1 models
> show #!14 models
> select #14/A:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/A:50-51
18 atoms, 17 bonds, 2 residues, 1 model selected
> show #14.1 models
> ui tool show Contacts
> contacts ignoreHiddenModels true
38036 contacts
> contacts delete
Exception in thread Thread-406 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 204, in _new_conn
sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 85, in create_connection
raise err
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
OSError: [Errno 65] No route to host
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 788, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connectionpool.py", line 493, in _make_request
conn.request(
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 500, in request
self.endheaders()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1058, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 996, in send
self.connect()
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 331, in connect
self.sock = self._new_conn()
^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/urllib3/connection.py", line 219, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError:
HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80): Failed to establish
a new connection: [Errno 65] No route to host
The above exception was the direct cause of the following exception:
[deleted to fit within ticket limits]
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
#5/A with 1 mismatch
Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [15]
Alignment identifier is bp6 [16]
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
#5/A with 1 mismatch
Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [16]
> alphafold fetch A0A1W9SC28 version 4 alignTo #5/A
AlphaFold prediction matching chain A
---
Chain| UniProt Id| RMSD| Length| Seen| % Id
A | A0A1W9SC28 | 6.09 | 392 | 404 | 37
Associated AlphaFold A0A1W9SC28 chain A to A0A1W9SC28 with 0 mismatches
> matchmaker #35 to #5/A
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 fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
A0A1W9SC28, chain A (#35), sequence alignment score = 832.9
RMSD between 246 pruned atom pairs is 1.019 angstroms; (across all 381 pairs:
6.089)
> rename #35 "AlphaFold A0A1W9SC28_9RICK - Glycosyltransferase 1 domain-
> containing protein - Rickettsiaceae bacterium 4572_127"
Alignment identifier is bp6 [17]
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
#5/A with 1 mismatch
Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [17]
> alphafold fetch A0A6I2UL91 version 4 alignTo #5/A
AlphaFold prediction matching chain A
---
Chain| UniProt Id| RMSD| Length| Seen| % Id
A | A0A6I2UL91 | 4.20 | 408 | 404 | 35
Associated AlphaFold A0A6I2UL91 chain A to A0A6I2UL91 with 0 mismatches
> matchmaker #36 to #5/A
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 fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
A0A6I2UL91, chain A (#36), sequence alignment score = 843.9
RMSD between 269 pruned atom pairs is 1.141 angstroms; (across all 387 pairs:
4.199)
> rename #36 "AlphaFold A0A6I2UL91_9FIRM - Glycosyltransferase family 4
> protein - Anaerovibrio slackiae"
> alphafold fetch G5H3T4 version 4 alignTo #5/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-G5H3T4-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch G5H3T4 version 4 alignTo #5/A
Fetching url https://alphafold.ebi.ac.uk/files/AF-G5H3T4-F1-model_v6.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch A0A346NJM2 version 4 alignTo #5/A
AlphaFold prediction matching chain A
---
Chain| UniProt Id| RMSD| Length| Seen| % Id
A | A0A346NJM2 | 6.59 | 379 | 404 | 36
Associated AlphaFold A0A346NJM2 chain A to A0A346NJM2 with 0 mismatches
> matchmaker #37 to #5/A
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 fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
A0A346NJM2, chain A (#37), sequence alignment score = 811.6
RMSD between 285 pruned atom pairs is 0.933 angstroms; (across all 372 pairs:
6.515)
> rename #37 "AlphaFold A0A346NJM2_9ALTE - Glycosyltransferase - Salinimonas
> sediminis"
> alphafold fetch A0A522RG72 version 4 alignTo #5/A
AlphaFold prediction matching chain A
---
Chain| UniProt Id| RMSD| Length| Seen| % Id
A | A0A522RG72 | 4.56 | 397 | 404 | 38
Associated AlphaFold A0A522RG72 chain A to A0A522RG72 with 0 mismatches
> matchmaker #38 to #5/A
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 fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
A0A522RG72, chain A (#38), sequence alignment score = 878
RMSD between 280 pruned atom pairs is 1.002 angstroms; (across all 385 pairs:
4.561)
> rename #38 "AlphaFold A0A522RG72_9BACT - Glycosyltransferase -
> Chitinophagaceae bacterium"
> hide #37 models
> hide #36 models
> hide #35 models
> hide #!1 models
> show #3 models
> hide #3 models
Alignment identifier is bp6 [18]
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
#5/A with 1 mismatch
Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [18]
Alignment identifier is bp6 [19]
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
A0A4B9BQ02 with 0 mismatches
Associated AlphaFold Q2QKP2 chain A to A0A4B9BQ02 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [19]
Alignment identifier is bp6 [20]
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches
Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches
[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
with 0 mismatches
Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
A0A4B9BQ02 with 0 mismatches
Associated AlphaFold Q2QKP2 chain A to A0A4B9BQ02 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [20]
> hide #38 models
> show #38 models
> hide #38 models
> show #!2 models
> show #!14 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
Drag select of 3 bonds, 1 atoms
> ui mousemode right translate
> ui mousemode right select
Drag select of 2 bonds
[Repeated 1 time(s)]Drag select of 1 bonds
Drag select of 1 atoms, 4 bonds
Drag select of 11 atoms, 4 residues, 11 bonds
Drag select of 1 atoms, 2 bonds
> ui mousemode right zoom
> select #14/A:404
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A
3292 atoms, 3376 bonds, 24 pseudobonds, 404 residues, 2 models selected
> show (#!14 & sel-residues & sidechain) target ab
> undo
> show (#!14 & sel-residues & sidechain) target ab
> undo
> delete show (#!14 & sel-residues & sidechain) target ab
Missing or invalid "atoms" argument: invalid atoms specifier
> delete show sidechains
Missing or invalid "atoms" argument: invalid atoms specifier
> delete show #14 selected sidechains
Missing or invalid "atoms" argument: invalid atoms specifier
> show #14.1 models
> hide #14.1 models
> hide #!2 models
> show #!2 models
> select add #14
3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #14
3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected
> select subtract #14
Nothing selected
> hide #!2 models
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!19 models
> show #!20 models
> hide #19.1 models
> hide #20.1 models
> show #20.1 models
> show #19.1 models
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> show #!21 models
> hide #21.1 models
> hide #!21 models
> show #21.1 models
> hide #!21 models
> open "/Users/aleezamughal/Downloads/fold_2026_05_15_15_51
> 2/fold_2026_05_15_15_51_model_0.cif"
Chain information for fold_2026_05_15_15_51_model_0.cif #39
---
Chain | Description
A | .
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
#15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
#17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
#15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
#17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Associated fold_2026_05_15_15_51_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP -
Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A
Computing secondary structure
> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_0.cif
Chain information for fold_gdp_bound_wbdp_model_0.cif #40
---
Chain | Description
A | .
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
#15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
#17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A,
fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
#15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
#17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A,
fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A,
fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
#19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
#!22/A, AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii #23/A,
AlphaFold Q2QKP2 #24/A, fold_2026_05_15_15_51_model_0.cif #39/A,
fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
#!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP
- Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Associated fold_gdp_bound_wbdp_model_0.cif chain A to
fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2_ESCFE - WbdP -
Escherichia fergusonii #23/A, AlphaFold Q2QKP2 #24/A,
fold_2026_05_15_15_51_model_0.cif #39/A, fold_gdp_bound_wbdp_model_0.cif #40/A
Computing secondary structure
> ui tool show Match→Align
> ui tool show Matchmaker
> matchmaker #39-40 to #1
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 AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_0.cif, chain A (#39), sequence alignment score =
2101.2
RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
2.582)
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_gdp_bound_wbdp_model_0.cif, chain A (#40), sequence alignment score =
2105.4
Alignment identifier is 38
Showing conservation header ("seq_conservation" residue attribute) for
alignment 38
Hiding conservation header for alignment 38
Chains used in RMSD evaluation for alignment 38: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #40/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 38
RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
1.657)
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain #39/A
Alignment identifier is 39/A
> sequence chain #40/A
Alignment identifier is 40/A
> ui mousemode right zoom
> ui mousemode right select
Drag select of 39 atoms, 49 residues, 36 bonds
Drag select of 161 atoms, 193 residues, 153 bonds
> select clear
Drag select of 160 atoms, 172 residues, 152 bonds
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> undo
[Repeated 1 time(s)]
> show (sel-residues & sidechain) target ab
> select add #39
4047 atoms, 3487 bonds, 493 residues, 2 models selected
> select subtract #39
723 atoms, 77 bonds, 88 residues, 1 model selected
> select add #40
3320 atoms, 3406 bonds, 405 residues, 1 model selected
> select subtract #40
Nothing selected
Drag select of 9 atoms, 11 residues, 7 bonds
> select add #39
3370 atoms, 3414 bonds, 414 residues, 2 models selected
> select subtract #39
46 atoms, 4 bonds, 9 residues, 1 model selected
> select add #39
3370 atoms, 3414 bonds, 414 residues, 2 models selected
> select add #40
6644 atoms, 6816 bonds, 810 residues, 2 models selected
> select subtract #40
3324 atoms, 3410 bonds, 405 residues, 1 model selected
> select subtract #39
Nothing selected
> ui mousemode right translate
> show (#39-40 & sidechain) target ab
> ui mousemode right zoom
> hide #39 models
> hide #40 models
> show #!21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!22 models
> show #!21 models
> show #!22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!22 models
> save "/Users/aleezamughal/Desktop/WbdP comparison + other
> glycosyltransferases 1.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ,
, , ] -> : Error while saving session data for 'tools' -> [, , , , , , , , , ,
, , , , , , , , , , ] ->
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 68, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ,
, , ] -> : Error while saving session data for 'tools' -> [, , , , , , , , , ,
, , , , , , , , , , ] ->
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save "/Users/aleezamughal/Desktop/wbdp comparisons.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ,
, , ] -> : Error while saving session data for 'tools' -> [, , , , , , , , , ,
, , , , , , , , , , ] ->
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 68, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x38620e250>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x3574e9ad0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x35e7efc90>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.color_actions.tool.ColorActions object at 0x155037f10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>]
-> <chimerax.blastprotein.ui.results.BlastProteinResults object at
0x14cd1af50>
ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ,
, , ] -> : Error while saving session data for 'tools' -> [, , , , , , , , , ,
, , , , , , , , , , ] ->
File
"/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 4 days, 9 hours, 42 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605080108
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.3
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.20.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.6
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.0
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.2
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.2
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.46.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
Change History (2)
comment:1 by , 8 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session save: 'BlastProteinResults' object has no attribute 'table' |
comment:2 by , 8 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Aleeza,
--Eric