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#20553 new defect

ChimeraX bug report submission

Reported by:	aleeza.mughal@…	Owned by:
Priority:	normal	Milestone:
Component:	Unassigned	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:
Project:

Description

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:  
  
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/FYN32J0BLRKN59QN/status
(Caused by
NewConnectionError("HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80):
Failed to establish a new connection: [Errno 65] No route to host"))  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

0 hydrogen bonds found  

> hide #!14 models

> select ::name="GDP"

168 atoms, 180 bonds, 6 residues, 6 models selected  

> hbonds delete

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

8 hydrogen bonds found  

> hide #!2 models

> show #!14 models

> hide #!14 models

> show #!2 models

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A

3296 atoms, 3380 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

17 hydrogen bonds found  

> hide #!2 models

> show #!14 models

> select #14/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:1-369

3006 atoms, 3086 bonds, 369 residues, 1 model selected  

> select #14/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #14/A:46-404

2929 atoms, 3004 bonds, 359 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  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

25 hydrogen bonds found  

> show #!2 models

> hide #!2 models

> hide #!14 models

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> show #!2 models

> hbonds delete

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

25 hydrogen bonds found  

> hide #14.1 models

> show #!14 models

> hide #!14 models

> hide #2 models

> show #2 models

> select #2/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:291-404

888 atoms, 901 bonds, 114 residues, 1 model selected  

> select #2/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:184-404

1778 atoms, 1822 bonds, 221 residues, 1 model selected  

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1-216

1785 atoms, 1836 bonds, 216 residues, 1 model selected  

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1-395

3221 atoms, 3305 bonds, 395 residues, 1 model selected  

> select #2/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A

3296 atoms, 3380 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

17 hydrogen bonds found  

> hide #!2 models

> show #!14 models

> show #14.1 models

> show #!2 models

> select add #2

3324 atoms, 3410 bonds, 17 pseudobonds, 405 residues, 2 models selected  

> select subtract #2

Nothing selected  

> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_1.cif

Chain information for fold_gdp_bound_wbdp_model_1.cif #15  
---  
Chain | Description  
A | .  
  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Associated fold_gdp_bound_wbdp_model_1.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  
Computing secondary structure  

> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_2.cif

Chain information for fold_gdp_bound_wbdp_model_2.cif #16  
---  
Chain | Description  
A | .  
  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Associated fold_gdp_bound_wbdp_model_2.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  
Computing secondary structure  

> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_3.cif

Chain information for fold_gdp_bound_wbdp_model_3.cif #17  
---  
Chain | Description  
A | .  
  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Associated fold_gdp_bound_wbdp_model_3.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  
Computing secondary structure  

> open
> /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_4.cif

Chain information for fold_gdp_bound_wbdp_model_4.cif #18  
---  
Chain | Description  
A | .  
  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.cif chain A to
fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Associated fold_gdp_bound_wbdp_model_4.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  
Computing secondary structure  

> ui tool show Match→Align

> ui tool show "Modeller Comparative"

> ui tool show Match→Align

> msa3d
> #!1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
0 fully populated columns  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #2/A, fold_2026_05_15_15_51_model_1.cif
#3/A, fold_2026_05_15_15_51_model_2.cif #4/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_2026_05_15_15_51_model_4.cif
#6/A, fold_2026_06_01_00_39_model_0.cif #7/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_2026_06_01_00_39_model_2.cif
#9/A, fold_2026_06_01_00_39_model_3.cif #10/A,
fold_2026_06_01_00_39_model_4.cif #11/A, AlphaFold A0A9Q6ZED9 #12/A, AlphaFold
A0A2W4UJ55 #13/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  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> ui tool show Match→Align

> msa3d
> #!1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
0 fully populated columns  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #2/A, fold_2026_05_15_15_51_model_1.cif
#3/A, fold_2026_05_15_15_51_model_2.cif #4/A,
fold_2026_05_15_15_51_model_3.cif #5/A, fold_2026_05_15_15_51_model_4.cif
#6/A, fold_2026_06_01_00_39_model_0.cif #7/A,
fold_2026_06_01_00_39_model_1.cif #8/A, fold_2026_06_01_00_39_model_2.cif
#9/A, fold_2026_06_01_00_39_model_3.cif #10/A,
fold_2026_06_01_00_39_model_4.cif #11/A, AlphaFold A0A9Q6ZED9 #12/A, AlphaFold
A0A2W4UJ55 #13/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  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> ui tool show Match→Align

> ui tool show Matchmaker

> matchmaker #3-13,15-18#!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_1.cif, chain A (#3), sequence alignment score =
2083.8  
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 21  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 21  
Hiding conservation header for alignment 21  
Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_2.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 21  
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 22  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 22  
Hiding conservation header for alignment 22  
Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_3.cif #5/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 22  
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 23  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 23  
Hiding conservation header for alignment 23  
Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_4.cif #6/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 23  
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 24  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 24  
Hiding conservation header for alignment 24  
Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_0.cif #7/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 24  
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 25  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 25  
Hiding conservation header for alignment 25  
Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_1.cif #8/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 25  
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 26  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 26  
Hiding conservation header for alignment 26  
Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_2.cif #9/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 26  
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 27  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 27  
Hiding conservation header for alignment 27  
Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_3.cif #10/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 27  
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 28  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 28  
Hiding conservation header for alignment 28  
Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_06_01_00_39_model_4.cif #11/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 28  
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 29  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 29  
Hiding conservation header for alignment 29  
Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
AlphaFold A0A9Q6ZED9 #12/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 29  
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_1.cif, chain A (#15), sequence alignment score =
2094.6  
Alignment identifier is 30  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 30  
Hiding conservation header for alignment 30  
Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_1.cif #15/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 30  
RMSD between 363 pruned atom pairs is 0.611 angstroms; (across all 404 pairs:
1.462)  
  
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_gdp_bound_wbdp_model_2.cif, chain A (#16), sequence alignment score =
2105.4  
Alignment identifier is 31  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 31  
Hiding conservation header for alignment 31  
Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_2.cif #16/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 31  
RMSD between 382 pruned atom pairs is 0.616 angstroms; (across all 404 pairs:
0.985)  
  
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_gdp_bound_wbdp_model_3.cif, chain A (#17), sequence alignment score =
2109  
Alignment identifier is 32  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 32  
Hiding conservation header for alignment 32  
Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_3.cif #17/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 32  
RMSD between 385 pruned atom pairs is 0.703 angstroms; (across all 404 pairs:
0.901)  
  
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_gdp_bound_wbdp_model_4.cif, chain A (#18), sequence alignment score =
2109  
Alignment identifier is 33  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 33  
Hiding conservation header for alignment 33  
Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_4.cif #18/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 33  
RMSD between 369 pruned atom pairs is 0.525 angstroms; (across all 404 pairs:
1.281)  
  
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_0.cif, chain A (#2), sequence alignment score =
2101.2  
Alignment identifier is 34  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 34  
Hiding conservation header for alignment 34  
Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 34  
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 (#14), sequence alignment score =
2105.4  
Alignment identifier is 35  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 35  
Hiding conservation header for alignment 35  
Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #14/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 35  
RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
1.657)  
  

> hide #!14 models

> hide #!2 models

> hide #15 models

> show #15 models

> hide #16 models

> hide #17 models

> hide #18 models

> ui tool show "Show Sequence Viewer"

> sequence chain #15/A

Alignment identifier is 15/A  

> sequence chain #16/A

Alignment identifier is 16/A  

> sequence chain #17/A

Alignment identifier is 17/A  

> sequence chain #18/A

Alignment identifier is 18/A  

> select #15/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #15/A

3292 atoms, 3376 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

25 hydrogen bonds found  

> show #!14 models

> hide #!14 models

> hide #!15 models

> show #!14 models

> select add #15

3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected  

> select subtract #15

Nothing selected  

> show #!15 models

> select add #15

3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected  

> select subtract #15

Nothing selected  

> hide #14.1 models

> hide #!15 models

> show #16 models

> hide #!14 models

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

Atom specifier selects no atoms  

> select #16/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #16/A:148-404

2065 atoms, 2113 bonds, 257 residues, 1 model selected  

> select #16/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #16/A

3292 atoms, 3376 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

21 hydrogen bonds found  

> hide #!16 models

> show #17 models

> select #17/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #17/A

3292 atoms, 3376 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

18 hydrogen bonds found  

> hide #!17 models

> show #18 models

> hide #18 models

> show #18 models

> show #!17 models

> select #17/A:191

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #17/A:191

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show #!16 models

> show #!15 models

> show #!14 models

> ui mousemode right translate

> show #!2 models

> ui mousemode right zoom

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #18 models

> show #14.1 models

> ui tool show "Selection Inspector"

> hide #!2 models

> select ::name="GDP"

280 atoms, 300 bonds, 10 residues, 10 models selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Distances

Exactly two atoms must be selected!  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #14/A:54-55

18 atoms, 19 bonds, 2 residues, 1 model selected  

> select #14/A:54

7 atoms, 7 bonds, 1 residue, 1 model selected  
Exactly two atoms must be selected!  
[Repeated 2 time(s)]

> select #14:GDP@O1

Nothing selected  

> select #14:54@CA and #14:GDP@O1

Expected a keyword  

> select #14:54@CA #14:GDP@O1

1 atom, 1 residue, 1 model selected  

> select ::name="GDP"

280 atoms, 300 bonds, 10 residues, 10 models selected  

> select #14:54@CA #14:GDP 1 PB @O1B

Expected a keyword  

> select #14:54@CA #14:GDP 1 @O1B

Expected a keyword  

> select #14:54@CA #14:GDP1 @O1B

1 atom, 1 residue, 1 model selected  

> select #14:GDP1 @O1B

Nothing selected  

> select #14:B GDP 1 PB O1B

Expected a keyword  

> select ligand

280 atoms, 300 bonds, 10 residues, 10 models selected  

> select #14:GDP@O1

Nothing selected  

> select #14:GDP@P

Nothing selected  

> select #14/B:GDP@PB

1 atom, 1 residue, 1 model selected  

> select select #14:54@CA #14/B:GDP@PB

Expected an objects specifier or a keyword  

> select select #14:54@CA and #14/B:GDP@PB

Expected an objects specifier or a keyword  

> select select #14:54@CA, #14/B:GDP@PB

Expected an objects specifier or a keyword  

> select select #14:54@CA,B:GDP@PB

Expected an objects specifier or a keyword  

> select select #14:54@CA,#14/B:GDP@PB

Expected an objects specifier or a keyword  

> select #14:54@CA,#14/B:GDP@PB

Expected an objects specifier or a keyword  

> select #14:54@CA and #14/B:GDP@PB

Expected a keyword  

> select #14:54@CA, #14/B:GDP@PB

Expected an objects specifier or a keyword  

> select #14:54@CA & #14/B:GDP@PB

Nothing selected  

> ui mousemode right translate

> rmsd #2 to #14

Number of atoms from first atom spec (3324) differs from number in second
(3320)  

> rmsd #2 to #14

Number of atoms from first atom spec (3324) differs from number in second
(3320)  

> rmsd #2 to #14 residues

Expected a keyword  

> rmsd #2 to #14 residue

Expected a keyword  

> rmsd #2 to #14

Number of atoms from first atom spec (3324) differs from number in second
(3320)  

> ui tool show "Minimize Structure"

> minimize #12

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to AlphaFold A0A9Q6ZED9 #12  
---  
notes | Termini for AlphaFold A0A9Q6ZED9 (#12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold A0A9Q6ZED9 #12/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold A0A9Q6ZED9 #12/A SER
404  
Chain-final residues that are not actual C termini:  
394 hydrogen bonds  
3276 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> show #12 models

> hide #!14 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> hide #12 models

> show #!2 models

> show #12 models

> hide #!2 models

> delete minimize #12

Missing or invalid "atoms" argument: invalid atoms specifier  

> undo minimize #12

Expected fewer arguments  

> undo

[Repeated 9 time(s)]

> show #!1 models

> hide #!1 models

> undo minimize #12

Expected fewer arguments  

> delete minimize #12

Missing or invalid "atoms" argument: invalid atoms specifier  

> minimize #12

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to AlphaFold A0A9Q6ZED9 #12  
---  
notes | Termini for AlphaFold A0A9Q6ZED9 (#12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold A0A9Q6ZED9 #12/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold A0A9Q6ZED9 #12/A SER
404  
Chain-final residues that are not actual C termini:  
481 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> 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 #19  
---  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
Computing secondary structure  

> hide #14.1 models

> show #14.1 models

> hide #14.1 models

> hide #!14 models

> hide #12 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 #20  
---  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
Computing secondary structure  

> hide #19 models

> show #19 models

> ui tool show Match→Align

> msa3d #19/A#20/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
32 residue pairs aligned  
404 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 19 | 20  
19 | 0.000 | 33.602  
20 | 33.602 | 0.000  
  
Overall RMSD: 33.602  
Sequence lengths: 404 404  
SDM (cutoff 5.0): -282.503  
Q-score: 0.008  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1:
fold_gdp_bound_wbdp_model_0.cif #19/A, fold_2026_05_15_15_51_model_0.cif #20/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> ui tool show Matchmaker

> matchmaker #19-20 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_gdp_bound_wbdp_model_0.cif, chain A (#19), sequence alignment score =
2105.4  
RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
1.657)  
  
Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
fold_2026_05_15_15_51_model_0.cif, chain A (#20), sequence alignment score =
2101.2  
Alignment identifier is 36  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 36  
Hiding conservation header for alignment 36  
Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
fold_2026_05_15_15_51_model_0.cif #20/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 36  
RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
2.582)  
  

> minimize #19

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to fold_gdp_bound_wbdp_model_0.cif
#19  
---  
notes | Termini for fold_gdp_bound_wbdp_model_0.cif (#19) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_gdp_bound_wbdp_model_0.cif #19/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_gdp_bound_wbdp_model_0.cif #19/A SER 404  
Chain-final residues that are not actual C termini:  
393 hydrogen bonds  
3288 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> ui mousemode right zoom

> select ::name="GDP"

348 atoms, 372 bonds, 12 residues, 12 models selected  

> open
> /Users/aleezamughal/Downloads/fold_2026_05_15_15_51/fold_2026_05_15_15_51_model_0.cif

Chain information for fold_2026_05_15_15_51_model_0.cif #21  
---  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
Computing secondary structure  

> hide #20 models

> hide #19 models

> select ::name="TYR"

5970 atoms, 6011 bonds, 463 residues, 21 models selected  

> show (#21 & sel-residues & sidechain) target ab

> show #19 models

> hide #21 models

> show (#19 & sel-residues & sidechain) target ab

> select add #19

12095 atoms, 12220 bonds, 845 residues, 21 models selected  

> select subtract #19

5487 atoms, 5526 bonds, 440 residues, 20 models selected  

> hide #19 models

> show #20 models

> show (#20 & sel-residues & sidechain) target ab

> ui tool show "Show Sequence Viewer"

> sequence chain #20/A

Alignment identifier is 20/A  

> select
> #20/A:14-29,44-63,78-84,101-110,125-129,140-142,145-147,150-165,175-184,203-206,210-216,231-233,235-247,268-279,282-284,293-301,318-326,339-341,355-365,374-403

1593 atoms, 1608 bonds, 194 residues, 1 model selected  

> select #20/A:245

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select #20/A:245

16 atoms, 16 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> show #18 models

> hide #18 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> minimize #20

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to fold_2026_05_15_15_51_model_0.cif
#20  
---  
notes | Termini for fold_2026_05_15_15_51_model_0.cif (#20) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_05_15_15_51_model_0.cif #20/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_05_15_15_51_model_0.cif #20/A SER 404  
Chain-final residues that are not actual C termini:  
385 hydrogen bonds  
3287 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.in.mol2 -fi
mol2 -o
/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.in.mol2);
atoms read (36), bonds read (36).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 166; net charge: -2`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Dock prep finished  

> show #19 models

> rmsd #19 to #20

Number of atoms from first atom spec (6608) differs from number in second
(6611)  

> rmsd #19:GDP to #20:GDP

RMSD between 40 atom pairs is 1.255  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

0 hydrogen bonds found  

> hide #!20 models

> show #!20 models

> select #20/A:1-2

41 atoms, 40 bonds, 2 residues, 1 model selected  

> select #20/A

6571 atoms, 6655 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

50 hydrogen bonds found  

> hide #19 models

> show #19 models

> hide #19 models

> hide #!20 models

> show #!20 models

> select add #20

6611 atoms, 6697 bonds, 50 pseudobonds, 405 residues, 2 models selected  

> select subtract #20

Nothing selected  

> show #19 models

> show #21 models

> hide #21 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #19 models

> hide #!20 models

> show #19 models

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

Atom specifier selects no atoms  

> ui tool show "Show Sequence Viewer"

> sequence chain #19/A

Alignment identifier is 19/A  

> select #19/A:404

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #19/A

6568 atoms, 6652 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

53 hydrogen bonds found  

> select add #19

6608 atoms, 6694 bonds, 53 pseudobonds, 405 residues, 2 models selected  

> select subtract #19

Nothing selected  

> show #!20 models

> hide #!19 models

> rmsd #19:GDP to #20:GDP

RMSD between 40 atom pairs is 1.255  

> rmsd #14:GDP to #2:GDP

RMSD between 28 atom pairs is 0.700  

> hide #!20 models

> show #!2 models

> show #7 models

> hide #7 models

> show #7 models

> show #!14 models

> ui mousemode right translate

> hide #!14 models

> show #!14 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #7 models

> show #21 models

> hide #21 models

> show #21 models

> hide #21 models

> hide #!2 models

> hide #2.1 models

> hide #!14 models

> show #21 models

> show #!20 models

> hide #21 models

> show #21 models

> hide #21 models

> hide #!20 models

> show #21 models

> hide #21 models

> show #!19 models

> hide #!19 models

> show #21 models

> hide #21 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 #22  
---  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
Computing secondary structure  

> show #21 models

> hide #21 models

> show #21 models

> ui tool show Matchmaker

> matchmaker #21-22 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 (#21), 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 (#22), sequence alignment score =
2105.4  
Alignment identifier is 37  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 37  
Hiding conservation header for alignment 37  
Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #22/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 37  
RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
1.657)  
  

> coulombic #21-22

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.in.mol2 -fi
mol2 -o
/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.in.mol2);
atoms read (36), bonds read (36).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 166; net charge: -2`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_2026_05_15_15_51_model_0.cif_A SES surface #21.1:
minimum, -20.05, mean -0.12, maximum 18.22  
Coulombic values for fold_gdp_bound_wbdp_model_0.cif_A SES surface #22.1:
minimum, -12.92, mean -0.15, maximum 18.97  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!21 models

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> ui mousemode right zoom

> hide #21.1 models

> show #21.1 models

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> view

[Repeated 2 time(s)]

> save /Users/aleezamughal/Desktop/image1.png supersample 3

> save /Users/aleezamughal/Desktop/image2.png supersample 3

> view

[Repeated 1 time(s)]

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/aleezamughal/Desktop/movie1.mp4

Movie saved to /Users/aleezamughal/Desktop/movie1.mp4  
  

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> movie record

> turn y 2 180

> wait 180

> movie encode /Users/aleezamughal/Desktop/movie1.mp4

Movie saved to /Users/aleezamughal/Desktop/movie1.mp4  
  

> show #!21 models

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> save /Users/aleezamughal/Desktop/image1.png supersample 3

> hide #!22 models

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> save /Users/aleezamughal/Desktop/image1.png supersample 3

> hide #!21 models

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> hide #22.1 models

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> ui tool show ViewDock

> ui tool show "Find Cavities"

> kvfinder #21-22

13 cavities found for fold_2026_05_15_15_51_model_0.cif #21  
fold_2026_05_15_15_51_model_0.cif Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
21.2.1 |  | 2150.28 | 1212.7 | 9955 | 9.49 | 3.39  
21.2.11 |  | 318.6 | 265.45 | 1475 | 8.03 | 2.57  
21.2.12 |  | 236.09 | 213 | 1093 | 3.7 | 1.08  
21.2.5 |  | 115.78 | 121.01 | 536 | 5.09 | 1.78  
21.2.8 |  | 96.98 | 114.53 | 449 | 4.2 | 1.59  
21.2.2 |  | 60.26 | 80.88 | 279 | 3.06 | 0.91  
21.2.4 |  | 34.99 | 47.21 | 162 | 1.9 | 0.55  
21.2.10 |  | 34.56 | 53.42 | 160 | 0 | 0  
21.2.9 |  | 30.46 | 38.72 | 141 | 2.24 | 0.96  
21.2.3 |  | 23.33 | 37.11 | 108 | 1.34 | 0.42  
21.2.13 |  | 21.38 | 34.14 | 99 | 3 | 1.2  
21.2.7 |  | 20.95 | 31.69 | 97 | 1.8 | 0.57  
21.2.6 |  | 11.88 | 22.51 | 55 | 0.6 | 0.16  
  
15 cavities found for fold_gdp_bound_wbdp_model_0.cif #22  
fold_gdp_bound_wbdp_model_0.cif Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
22.2.4 |  | 1932.12 | 1131.17 | 8945 | 9.1 | 3.35  
22.2.8 |  | 249.7 | 203.45 | 1156 | 4.24 | 1.37  
22.2.3 |  | 159.41 | 160.61 | 738 | 4.84 | 1.18  
22.2.12 |  | 91.58 | 106.5 | 424 | 5.16 | 1.8  
22.2.6 |  | 42.98 | 62.43 | 199 | 2.47 | 0.69  
22.2.13 |  | 33.7 | 49.87 | 156 | 3.84 | 1.55  
22.2.9 |  | 29.81 | 49.21 | 138 | 4.24 | 2.13  
22.2.1 |  | 26.35 | 44.29 | 122 | 0 | 0  
22.2.10 |  | 20.74 | 41.19 | 96 | 0 | 0  
22.2.14 |  | 20.52 | 29.2 | 95 | 1.8 | 0.53  
22.2.7 |  | 19.66 | 27.87 | 91 | 2.16 | 0.68  
22.2.15 |  | 18.79 | 30.53 | 87 | 1.8 | 0.5  
22.2.11 |  | 12.31 | 29.54 | 57 | 0 | 0  
22.2.2 |  | 9.5 | 20.34 | 44 | 0.85 | 0.34  
22.2.5 |  | 6.26 | 13.53 | 29 | 0.6 | 0.08  
  

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> select add #22

15697 atoms, 3406 bonds, 420 residues, 17 models selected  

> select subtract #22

1 model selected  

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> show #!21 models

> hide #!21 models

Cell requested for row 23 is out of bounds for table with 28 rows! Resizing
table model.  

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> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

Atom specifier selects no atoms  

> ui tool show "Show Sequence Viewer"

> sequence chain #20/A

Destroying pre-existing alignment with identifier 20/A  
Alignment identifier is 20/A  

> sequence chain #!21/A

Alignment identifier is 21/A  

> sequence chain #!22/A

Alignment identifier is 22/A  

> select #!22/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #!22/A:181-404

1796 atoms, 1840 bonds, 224 residues, 1 model selected  

> select #!22/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #!22/A

3292 atoms, 3376 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

25 hydrogen bonds found  

> hide #!22.2 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!22 models

> show #!22.2 models

> hide #!22.2 models

> hide #!22 models

> show #!21 models

> hide #!21.2 models

> select #!21/A:404

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #!21/A

3296 atoms, 3380 bonds, 404 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel interModel false saltOnly true reveal true

17 hydrogen bonds found  

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!22 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!22 models

> ui tool show "Modeller Comparative"

> hide #!21 models

> show #!1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!21 models

> hide #!1 models

> hide #21.1 models

> show #!21.2 models

> hide #21.2.1 models

> show #21.2.1 models

> hide #!21.2 models

> show #21.1 models

> hide #!21 models

> show #!1 models

> show #!2 models

> hide #!2 models

> ui tool show "Blast Protein"

> blastprotein #!1/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
> 100 version 4 name bp4

Webservices job id: 18VPL69O9YDHF6OF  
Webservices job finished: 18VPL69O9YDHF6OF  
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.  
  

> ui tool show "Blast Protein"

> blastprotein #12/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
> 100 version 4 name bp5

Webservices job id: KHHXL2DK7SH44YG9  
Exception in thread Thread-5295 (_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 488, in _make_request  
raise new_e  
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 464, in _make_request  
self._validate_conn(conn)  
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 1106, in _validate_conn  
conn.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 759, in connect  
self.sock = 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:
HTTPSConnection(host='webservices.rbvi.ucsf.edu', port=443): 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 503, in urlopen  
return self.urlopen(method, redirect_location, **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 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:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url: /cxservices/api/v1/chimerax/jobs/KHHXL2DK7SH44YG9/status
(Caused by
NewConnectionError("HTTPSConnection(host='webservices.rbvi.ucsf.edu',
port=443): Failed to establish a new connection: [Errno 65] No route to
host"))  

> ui tool show "Blast Protein"

> blastprotein #5/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 4 name bp6

Webservices job id: 6O86EWCZ2TXMDOQW  

> save "/Users/aleezamughal/Desktop/WbdP analysis.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.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<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.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>:
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<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.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<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.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>:
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
<chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
<chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
<chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
<chimerax.log.tool.Log object at 0x12c89b950>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
<chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
<chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
<chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
<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.  
  
Webservices job finished: 6O86EWCZ2TXMDOQW  
Alignment identifier is bp6 [1]  
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  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp6 [1]  

> alphafold fetch Q2QKP2 version 4 alignTo #5/A

Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json  
Fetching compressed AlphaFold Q2QKP2 from
https://alphafold.ebi.ac.uk/files/AF-Q2QKP2-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | Q2QKP2 | 2.45 | 404 | 404 | 100   
  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_1.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_2.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_3.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_4.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
chain A with 1 mismatch  
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 #23/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A  
Associated AlphaFold Q2QKP2 chain A to Q2QKP2 with 0 mismatches  

> matchmaker #23 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
Q2QKP2, chain A (#23), sequence alignment score = 2105.3  
RMSD between 367 pruned atom pairs is 0.622 angstroms; (across all 404 pairs:
2.454)  
  

> select #!1/A:62 #2/A:62 #3/A:62 #4/A:62 #5/A:62 #6/A:62 #7/A:62 #8/A:62
> #9/A:62 #10/A:62 #11/A:62 #12/A:62 #14/A:62 #15/A:62 #16/A:62 #17/A:62
> #18/A:62 #19/A:62 #20/A:62 #!21/A:62 #!22/A:62

201 atoms, 180 bonds, 21 residues, 21 models selected  

> select #!1/A:62 #2/A:62 #3/A:62 #4/A:62 #5/A:62 #6/A:62 #7/A:62 #8/A:62
> #9/A:62 #10/A:62 #11/A:62 #12/A:62 #14/A:62 #15/A:62 #16/A:62 #17/A:62
> #18/A:62 #19/A:62 #20/A:62 #!21/A:62 #!22/A:62

201 atoms, 180 bonds, 21 residues, 21 models selected  
Bp6 [1] [ID: bp6 [1]] region #5/A [62] RMSD: 8.615  
  

> alphafold fetch Q2QKP2 version 4 alignTo #5/A

AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | Q2QKP2 | 2.45 | 404 | 404 | 100   
  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
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 #23/A, AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
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 #23/A, AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
chain A with 1 mismatch  
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 #23/A, AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
chain A with 1 mismatch  
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 #23/A, AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_1.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_2.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_3.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_4.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
chain A with 1 mismatch  
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 #23/A,
AlphaFold Q2QKP2 #24/A  
Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
A with 1 mismatch  
Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold
Q2QKP2 #24/A  

> matchmaker #24 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
Q2QKP2, chain A (#24), sequence alignment score = 2105.3  
RMSD between 367 pruned atom pairs is 0.622 angstroms; (across all 404 pairs:
2.454)  
  

> hide #24 models

> rename #23 "AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii"

Alignment identifier is bp6 [2]  
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 [2]  

> alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A

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 #5/A

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 #5/A

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 #5/A

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 #5/A

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 #5/A

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 #5/A

Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  
Alignment identifier is bp6 [3]  
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 [3]  

> surface (#!1 & sel)

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1.2 models

> hide #!1 models

> select add #24

3492 atoms, 3555 bonds, 425 residues, 25 models selected  

> select subtract #24

201 atoms, 180 bonds, 21 residues, 24 models selected  

> select add #24

3492 atoms, 3555 bonds, 425 residues, 25 models selected  

> show #24 models

> hide #23 models

> surface (#24 & sel)

> ui tool show "Color Actions"

> coulombic sel & #!24

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q2QKP2_A SES surface #24.1: minimum, -14.42,
mean 0.04, maximum 14.67  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #24.1 models

> select subtract #24

201 atoms, 180 bonds, 21 residues, 25 models selected  

> hide #!24 models

> alphafold fetch A0A737Y3F8 version 4 alignTo #5/A

Fetching compressed AlphaFold A0A737Y3F8 from
https://alphafold.ebi.ac.uk/files/AF-A0A737Y3F8-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A0A737Y3F8 | 1.92 | 404 | 404 | 67   
  
Associated AlphaFold A0A737Y3F8 chain A to A0A737Y3F8 with 0 mismatches  

> matchmaker #25 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
A0A737Y3F8, chain A (#25), sequence alignment score = 1613.7  
RMSD between 371 pruned atom pairs is 0.726 angstroms; (across all 404 pairs:
1.918)  
  

> rename #25 "AlphaFold A0A737Y3F8_SALER - Glycosyltransferase family 4
> protein - Salmonella enterica subsp. salamae serovar 30:1, z28:z6"

> alphafold fetch G5RX88 version 4 alignTo #5/A

Fetching compressed AlphaFold G5RX88 from
https://alphafold.ebi.ac.uk/files/AF-G5RX88-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | G5RX88 | 2.16 | 404 | 404 | 67   
  
Associated AlphaFold G5RX88 chain A to G5RX88 with 0 mismatches  

> matchmaker #26 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
G5RX88, chain A (#26), sequence alignment score = 1621.6  
RMSD between 367 pruned atom pairs is 0.659 angstroms; (across all 404 pairs:
2.156)  
  

> rename #26 "AlphaFold G5RX88_SALET - Mannosyltransferase - Salmonella"

> rename #26 "AlphaFold G5RX88_SALET - Mannosyltransferase - Salmonella
> enterica subsp. enterica serovar Urbana str. R8-2977"

> alphafold fetch A0A5X6ERK5 version 4 alignTo #5/A

Fetching compressed AlphaFold A0A5X6ERK5 from
https://alphafold.ebi.ac.uk/files/AF-A0A5X6ERK5-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A0A5X6ERK5 | 2.42 | 404 | 404 | 67   
  
Associated AlphaFold A0A5X6ERK5 chain A to A0A5X6ERK5 with 0 mismatches  

> matchmaker #27 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
A0A5X6ERK5, chain A (#27), sequence alignment score = 1625  
RMSD between 369 pruned atom pairs is 0.690 angstroms; (across all 404 pairs:
2.422)  
  

> rename #27 "AlphaFold A0A5X6ERK5_SALET - Glycosyltransferase - Salmonella
> enterica subsp. enterica serovar Aqua"

> alphafold fetch Q5UHC2 version 4 alignTo #5/A

AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | Q5UHC2 | 2.05 | 404 | 404 | 67   
  
Associated AlphaFold Q5UHC2 chain A to Q5UHC2 with 0 mismatches  

> matchmaker #28 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
Q5UHC2, chain A (#28), sequence alignment score = 1602.3  
RMSD between 372 pruned atom pairs is 0.652 angstroms; (across all 404 pairs:
2.049)  
  

> rename #28 "AlphaFold Q5UHC2_SALET - Glycosyltransferase - Salmonella
> enterica subsp. enterica serovar Urbana"

Alignment identifier is bp6 [4]  
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 [4]  

> alphafold fetch Q5UHD5 version 4 alignTo #5/A

Fetching compressed AlphaFold Q5UHD5 from
https://alphafold.ebi.ac.uk/files/AF-Q5UHD5-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | Q5UHD5 | 1.93 | 404 | 404 | 60   
  
Associated AlphaFold Q5UHD5 chain A to Q5UHD5 with 0 mismatches  

> matchmaker #29 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
Q5UHD5, chain A (#29), sequence alignment score = 1498.7  
RMSD between 367 pruned atom pairs is 0.730 angstroms; (across all 404 pairs:
1.932)  
  

> rename #29 "AlphaFold Q5UHD5_CITFR - Glycosyltransferase - Citrobacter
> freundii"

Alignment identifier is bp6 [5]  
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 [5]  

> alphafold fetch A4SVM0 version 4 alignTo #5/A

AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A4SVM0 | 1.71 | 409 | 404 | 44   
  
Associated AlphaFold A4SVM0 chain A to A4SVM0 with 0 mismatches  

> matchmaker #30 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
A4SVM0, chain A (#30), sequence alignment score = 1151.6  
RMSD between 348 pruned atom pairs is 0.893 angstroms; (across all 403 pairs:
1.714)  
  

> rename #30 "AlphaFold A4SVM0_POLAQ - Glycosyltransferase group 1 - "

> rename #30 "AlphaFold A4SVM0_POLAQ - Glycosyltransferase group 1 -
> Polynucelobacter asymbioticus (strain DSM 18221 / CIP 109841 /
> QLW-P1DMWA-1)"

Alignment identifier is bp6 [6]  
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 [6]  

> alphafold fetch A0A2M8K035 version 4 alignTo #5/A

Fetching compressed AlphaFold A0A2M8K035 from
https://alphafold.ebi.ac.uk/files/AF-A0A2M8K035-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A0A2M8K035 | 2.33 | 406 | 404 | 46   
  
Associated AlphaFold A0A2M8K035 chain A to A0A2M8K035 with 0 mismatches  

> matchmaker #31 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
A0A2M8K035, chain A (#31), sequence alignment score = 1160.9  
RMSD between 327 pruned atom pairs is 0.874 angstroms; (across all 400 pairs:
2.327)  
  

> hide #30 models

> hide #29 models

> hide #28 models

> hide #27 models

> hide #26 models

> hide #25 models

> show #!1 models

> rename #31 "AlphaFold A0A2M8K035_9GAMM - Glycosyltransferase 1 domain-
> containing protein - Marinomonas sp. BSi20584"

Alignment identifier is bp6 [7]  
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 [7]  

> alphafold fetch A0A1A3L386 version 4 alignTo #5/A

Fetching compressed AlphaFold A0A1A3L386 from
https://alphafold.ebi.ac.uk/files/AF-A0A1A3L386-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A0A1A3L386 | 5.42 | 409 | 404 | 38   
  
Associated AlphaFold A0A1A3L386 chain A to A0A1A3L386 with 0 mismatches  

> matchmaker #32 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
A0A1A3L386, chain A (#32), sequence alignment score = 988.6  
RMSD between 310 pruned atom pairs is 0.918 angstroms; (across all 397 pairs:
5.422)  
  

> rename #32 "AlphaFold A0A1A3L386_MYCAS - Glycosyltransferase 1 domain-
> containing protein - Mycobacterium asiaticum"

Alignment identifier is bp6 [8]  
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 [8]  
Alignment identifier is bp6 [9]  
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 [9]  
Alignment identifier is bp6 [10]  
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 [10]  

> alphafold fetch C6E0L3 version 4 alignTo #5/A

Fetching compressed AlphaFold C6E0L3 from
https://alphafold.ebi.ac.uk/files/AF-C6E0L3-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | C6E0L3 | 3.38 | 413 | 404 | 38   
  
Associated AlphaFold C6E0L3 chain A to C6E0L3 with 0 mismatches  

> matchmaker #33 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
C6E0L3, chain A (#33), sequence alignment score = 954.7  
RMSD between 293 pruned atom pairs is 1.058 angstroms; (across all 401 pairs:
3.394)  
  

> rename #33 "AlphaFold C6E0L3_GEOSM - Glycosyltransferase group 1 - Geobacter
> sp. (strain M21)"

Alignment identifier is bp6 [11]  
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 [11]  

> hide #31 models

> hide #32 models

> hide #33 models

Alignment identifier is bp6 [12]  
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 [12]  

> alphafold fetch A0A4R7CL53 version 4 alignTo #5/A

Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4R7CL53-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> alphafold fetch A0A4R7CL53 version 4 alignTo #5/A

Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4R7CL53-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  
Alignment identifier is bp6 [13]  
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 [13]  

> alphafold fetch A0A257L694 version 4 alignTo #5/A

Fetching compressed AlphaFold A0A257L694 from
https://alphafold.ebi.ac.uk/files/AF-A0A257L694-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | A0A257L694 | 4.03 | 397 | 404 | 34   
  
Associated AlphaFold A0A257L694 chain A to A0A257L694 with 0 mismatches  

> matchmaker #34 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
A0A257L694, chain A (#34), sequence alignment score = 916.9  
RMSD between 257 pruned atom pairs is 0.949 angstroms; (across all 393 pairs:
4.032)  
  

> rename #34 "AlphaFold A0A257L694_9BACT - Glycosyltransferase 1 domain-
> containing protein - Bacteroidetes bacterium B1(2017)"

Alignment identifier is bp6 [14]  
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 [14]  

> alphafold fetch R6HU74 version 4 alignTo #5/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 #5/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 #5/A

Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> alphafold fetch K2ACG0 version 4 alignTo #5/A

Fetching compressed AlphaFold K2ACG0 from
https://alphafold.ebi.ac.uk/files/AF-K2ACG0-F1-model_v6.cif  
AlphaFold prediction matching chain A  
---  
Chain| UniProt Id| RMSD| Length| Seen| % Id  
A | K2ACG0 | 4.98 | 405 | 404 | 36   
  

> 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
K2ACG0, chain A (#35), sequence alignment score = 866.8  
RMSD between 279 pruned atom pairs is 1.136 angstroms; (across all 387 pairs:
4.977)  
  

> delete #35

> hide #34 models

Alignment identifier is bp6 [15]  
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 [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

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#20553 new defect

ChimeraX bug report submission

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