Opened 7 months ago

Closed 7 months ago

#17153 closed defect (fixed)

Web services down

Reported by: grzesiak1@… Owned by: Zach Pearson
Priority: major Milestone:
Component: Web Services Version:
Keywords: Cc: pett, julio.bonilla@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Anytime I try: sequence align [#model_1/antigen_chain1, #model_2/antigen_chain_2] program clustalOmega 
I get a "cannot create alignment of zero sequences" error, even on sequences I tried out earlier this week without any issue previously.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py

Traceback (most recent call last):  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 2, in <module>  
import pandas as pd  
ModuleNotFoundError: No module named 'pandas'  
  
Error opening python file
C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py  

> pip install pandas

> pip install pyyaml

> open
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py

executed chimeraX_find_EP_and_surface.py  

> find_epitopes_and_surfaces
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_Ag_test.yaml

PDB Dict: {'pdb': {'7UST': {'A': {'id': 'antigen1', 'include': True}, 'B':
{'id': 'ab_light', 'include': True}}, '6OHG': {'A': {'id': 'antigen2',
'include': True}, 'B': {'id': 'ab_light', 'include': True}, 'C': {'id':
'ab_heavy', 'include': True}}, '7UC8': {'A': {'id': 'antigen3', 'include':
True}, 'H': {'id': 'ab_heavy', 'include': True}}, '7USS': {'A': {'id':
'antigen4', 'include': True}}, '7USR': {'A': {'id': 'antigen5', 'include':
True}}, '7UVH': {'A': {'id': 'ab_heavy', 'include': True}, 'B': {'id':
'ab_light', 'include': True}, 'C': {'id': 'antigen6', 'include': True}}},
'destination': {'output_dir': 'C:/Users/grzesiak1/Downloads/chimerax_outputs',
'output_yaml_name': 'output.yaml'}}  

> open 7UST fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UST bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F5 [more
info...]  
  
Chain information for 7UST bioassembly 1 #1  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | Nanobody F5  
  
Non-standard residues in 7UST bioassembly 1 #1  
---  
SO4 — sulfate ion  
  
Opened 1 biological assemblies for 7UST  
Opened PDB: 7UST, Chain: A, Antigen ID: antigen1  

> open 6OHG fromDatabase rcsb_bio format mmcif maxAssemblies 1

6OHG bioassembly 1 title:  
Structure of Plasmodium falciparum vaccine candidate Pfs230D1M in complex with
the Fab of a transmission blocking antibody [more info...]  
  
Chain information for 6OHG bioassembly 1 #2  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | 4F12 Light Chain  
C | 4F12 Heavy chain  
  
Non-standard residues in 6OHG bioassembly 1 #2  
---  
ACY — acetic acid  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MOH — methanol  
PDO — 1,3-propandiol  
  
Opened 1 biological assemblies for 6OHG  
Opened PDB: 6OHG, Chain: A, Antigen ID: antigen2  

> open 7UC8 fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UC8 bioassembly 1 title:  
Pfs230 D1 domain in complex with 230AS-73 [more info...]  
  
Chain information for 7UC8 bioassembly 1 #3  
---  
Chain | Description  
A | Gametocyte surface protein P230  
H | 230AS-73  
  
Opened 1 biological assemblies for 7UC8  
Opened PDB: 7UC8, Chain: A, Antigen ID: antigen3  

> open 7USS fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USS bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 Pro-D1D2 - Structure of the first two
6-cysteine domains with N-terminal extension [more info...]  
  
Chain information for 7USS bioassembly 1 #4  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USS bioassembly 1 #4  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
K — potassium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USS  
Opened PDB: 7USS, Chain: A, Antigen ID: antigen4  

> open 7USR fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USR bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1D2 - Structure of the first two
6-cysteine domains [more info...]  
  
Chain information for 7USR bioassembly 1 #5  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USR bioassembly 1 #5  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USR  
Opened PDB: 7USR, Chain: A, Antigen ID: antigen5  

> open 7UVH fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UVH bioassembly 1 title:  
Pfs230 domain 1 bound by RUPA-32 Fab [more info...]  
  
Chain information for 7UVH bioassembly 1 #6  
---  
Chain | Description  
A | RUPA-32 Fab Heavy Chain  
B | RUPA-32 Fab Light Chain  
C | Gametocyte surface protein P230  
  
Non-standard residues in 7UVH bioassembly 1 #6  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NH4 — ammonium ion  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
Opened 1 biological assemblies for 7UVH  
Opened PDB: 7UVH, Chain: C, Antigen ID: antigen6  
{'7UST': '#1/A', '6OHG': '#2/A', '7UC8': '#3/A', '7USS': '#4/A', '7USR':
'#5/A', '7UVH': '#6/C'}  
{'7UST': '#1/B', '6OHG': '#2/B,C', '7UC8': '#3/H', '7USS': [], '7USR': [],
'7UVH': '#6/A,B'}  
Running sequence alignment with command: sequence align
#1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega  

> sequence align #1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 349, in main  
align_antigens(session, antigen_chain_references)  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 85, in align_antigens  
run(session, alignment_command)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-30 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence align #1/A,#2/A program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-49 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> close session

> open
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py

FYI: command is replacing existing command: "find_epitopes_and_surfaces"  
executed chimeraX_find_EP_and_surface.py  

> sequence align #1/A,#2/A program clustalOmega

Missing or invalid "seqSource" argument: Expected alignment-id or sequences  

> find_epitopes_and_surfaces
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_Ag_test.yaml

PDB Dict: {'pdb': {'7UST': {'A': {'id': 'antigen1', 'include': True}, 'B':
{'id': 'ab_light', 'include': True}}, '6OHG': {'A': {'id': 'antigen2',
'include': True}, 'B': {'id': 'ab_light', 'include': True}, 'C': {'id':
'ab_heavy', 'include': True}}, '7UC8': {'A': {'id': 'antigen3', 'include':
True}, 'H': {'id': 'ab_heavy', 'include': True}}, '7USS': {'A': {'id':
'antigen4', 'include': True}}, '7USR': {'A': {'id': 'antigen5', 'include':
True}}, '7UVH': {'A': {'id': 'ab_heavy', 'include': True}, 'B': {'id':
'ab_light', 'include': True}, 'C': {'id': 'antigen6', 'include': True}}},
'destination': {'output_dir': 'C:/Users/grzesiak1/Downloads/chimerax_outputs',
'output_yaml_name': 'output.yaml'}}  

> open 7UST fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UST bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F5 [more
info...]  
  
Chain information for 7UST bioassembly 1 #1  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | Nanobody F5  
  
Non-standard residues in 7UST bioassembly 1 #1  
---  
SO4 — sulfate ion  
  
Opened 1 biological assemblies for 7UST  
Opened PDB: 7UST, Chain: A, Antigen ID: antigen1  

> open 6OHG fromDatabase rcsb_bio format mmcif maxAssemblies 1

6OHG bioassembly 1 title:  
Structure of Plasmodium falciparum vaccine candidate Pfs230D1M in complex with
the Fab of a transmission blocking antibody [more info...]  
  
Chain information for 6OHG bioassembly 1 #2  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | 4F12 Light Chain  
C | 4F12 Heavy chain  
  
Non-standard residues in 6OHG bioassembly 1 #2  
---  
ACY — acetic acid  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MOH — methanol  
PDO — 1,3-propandiol  
  
Opened 1 biological assemblies for 6OHG  
Opened PDB: 6OHG, Chain: A, Antigen ID: antigen2  

> open 7UC8 fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UC8 bioassembly 1 title:  
Pfs230 D1 domain in complex with 230AS-73 [more info...]  
  
Chain information for 7UC8 bioassembly 1 #3  
---  
Chain | Description  
A | Gametocyte surface protein P230  
H | 230AS-73  
  
Opened 1 biological assemblies for 7UC8  
Opened PDB: 7UC8, Chain: A, Antigen ID: antigen3  

> open 7USS fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USS bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 Pro-D1D2 - Structure of the first two
6-cysteine domains with N-terminal extension [more info...]  
  
Chain information for 7USS bioassembly 1 #4  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USS bioassembly 1 #4  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
K — potassium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USS  
Opened PDB: 7USS, Chain: A, Antigen ID: antigen4  

> open 7USR fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USR bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1D2 - Structure of the first two
6-cysteine domains [more info...]  
  
Chain information for 7USR bioassembly 1 #5  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USR bioassembly 1 #5  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USR  
Opened PDB: 7USR, Chain: A, Antigen ID: antigen5  

> open 7UVH fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UVH bioassembly 1 title:  
Pfs230 domain 1 bound by RUPA-32 Fab [more info...]  
  
Chain information for 7UVH bioassembly 1 #6  
---  
Chain | Description  
A | RUPA-32 Fab Heavy Chain  
B | RUPA-32 Fab Light Chain  
C | Gametocyte surface protein P230  
  
Non-standard residues in 7UVH bioassembly 1 #6  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NH4 — ammonium ion  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
Opened 1 biological assemblies for 7UVH  
Opened PDB: 7UVH, Chain: C, Antigen ID: antigen6  
Running sequence alignment with command: sequence align
#1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega  

> sequence align #1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 349, in main  
align_antigens(session, antigen_chain_references)  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 85, in align_antigens  
run(session, alignment_command)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-76 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> close session

> open
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py

FYI: command is replacing existing command: "find_epitopes_and_surfaces"  
executed chimeraX_find_EP_and_surface.py  

> find_epitopes_and_surfaces
> C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_Ag_test.yaml

PDB Dict: {'pdb': {'7UST': {'A': {'id': 'antigen1', 'include': True}, 'B':
{'id': 'ab_light', 'include': True}}, '6OHG': {'A': {'id': 'antigen2',
'include': True}, 'B': {'id': 'ab_light', 'include': True}, 'C': {'id':
'ab_heavy', 'include': True}}, '7UC8': {'A': {'id': 'antigen3', 'include':
True}, 'H': {'id': 'ab_heavy', 'include': True}}, '7USS': {'A': {'id':
'antigen4', 'include': True}}, '7USR': {'A': {'id': 'antigen5', 'include':
True}}, '7UVH': {'A': {'id': 'ab_heavy', 'include': True}, 'B': {'id':
'ab_light', 'include': True}, 'C': {'id': 'antigen6', 'include': True}}},
'destination': {'output_dir': 'C:/Users/grzesiak1/Downloads/chimerax_outputs',
'output_yaml_name': 'output.yaml'}}  

> open 7UST fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UST bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F5 [more
info...]  
  
Chain information for 7UST bioassembly 1 #1  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | Nanobody F5  
  
Non-standard residues in 7UST bioassembly 1 #1  
---  
SO4 — sulfate ion  
  
Opened 1 biological assemblies for 7UST  
Opened PDB: 7UST, Chain: A, Antigen ID: antigen1  

> open 6OHG fromDatabase rcsb_bio format mmcif maxAssemblies 1

6OHG bioassembly 1 title:  
Structure of Plasmodium falciparum vaccine candidate Pfs230D1M in complex with
the Fab of a transmission blocking antibody [more info...]  
  
Chain information for 6OHG bioassembly 1 #2  
---  
Chain | Description  
A | Gametocyte surface protein P230  
B | 4F12 Light Chain  
C | 4F12 Heavy chain  
  
Non-standard residues in 6OHG bioassembly 1 #2  
---  
ACY — acetic acid  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MOH — methanol  
PDO — 1,3-propandiol  
  
Opened 1 biological assemblies for 6OHG  
Opened PDB: 6OHG, Chain: A, Antigen ID: antigen2  

> open 7UC8 fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UC8 bioassembly 1 title:  
Pfs230 D1 domain in complex with 230AS-73 [more info...]  
  
Chain information for 7UC8 bioassembly 1 #3  
---  
Chain | Description  
A | Gametocyte surface protein P230  
H | 230AS-73  
  
Opened 1 biological assemblies for 7UC8  
Opened PDB: 7UC8, Chain: A, Antigen ID: antigen3  

> open 7USS fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USS bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 Pro-D1D2 - Structure of the first two
6-cysteine domains with N-terminal extension [more info...]  
  
Chain information for 7USS bioassembly 1 #4  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USS bioassembly 1 #4  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
K — potassium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USS  
Opened PDB: 7USS, Chain: A, Antigen ID: antigen4  

> open 7USR fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USR bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1D2 - Structure of the first two
6-cysteine domains [more info...]  
  
Chain information for 7USR bioassembly 1 #5  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USR bioassembly 1 #5  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USR  
Opened PDB: 7USR, Chain: A, Antigen ID: antigen5  

> open 7UVH fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UVH bioassembly 1 title:  
Pfs230 domain 1 bound by RUPA-32 Fab [more info...]  
  
Chain information for 7UVH bioassembly 1 #6  
---  
Chain | Description  
A | RUPA-32 Fab Heavy Chain  
B | RUPA-32 Fab Light Chain  
C | Gametocyte surface protein P230  
  
Non-standard residues in 7UVH bioassembly 1 #6  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NH4 — ammonium ion  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
Opened 1 biological assemblies for 7UVH  
Opened PDB: 7UVH, Chain: C, Antigen ID: antigen6  
Running sequence alignment with command: sequence align
#1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega  

> sequence align #1/A,#2/A,#3/A,#4/A,#5/A,#6/C program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 349, in main  
align_antigens(session, antigen_chain_references)  
File
"C:/Users/grzesiak1/abag_seq_analysisandvis/abag_seq_analysisandvis/chimeraX/chimeraX_find_EP_and_surface.py",
line 85, in align_antigens  
run(session, alignment_command)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-102 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> close session

> open 7UVH fromDatabase rcsb_bio format mmcif maxAssemblies 1

7UVH bioassembly 1 title:  
Pfs230 domain 1 bound by RUPA-32 Fab [more info...]  
  
Chain information for 7UVH bioassembly 1 #1  
---  
Chain | Description  
A | RUPA-32 Fab Heavy Chain  
B | RUPA-32 Fab Light Chain  
C | Gametocyte surface protein P230  
  
Non-standard residues in 7UVH bioassembly 1 #1  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NH4 — ammonium ion  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
Opened 1 biological assemblies for 7UVH  

> open 7USR fromDatabase rcsb_bio format mmcif maxAssemblies 1

7USR bioassembly 1 title:  
Plasmodium falciparum protein Pfs230 D1D2 - Structure of the first two
6-cysteine domains [more info...]  
  
Chain information for 7USR bioassembly 1 #2  
---  
Chain | Description  
A | Gametocyte surface protein P230  
  
Non-standard residues in 7USR bioassembly 1 #2  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
Opened 1 biological assemblies for 7USR  

> sequence align #1/C,#2/A program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-119 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> select add #1

4701 atoms, 4731 bonds, 673 residues, 1 model selected  

> select add #2

7301 atoms, 7080 bonds, 1 pseudobond, 1262 residues, 3 models selected  

> sequence align #1/C,#2/A program clustalOmega

Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 372, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
ValueError: Cannot create alignment of zero sequences  
  
ValueError: Cannot create alignment of zero sequences  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 85, in __init__  
raise ValueError("Cannot create alignment of zero sequences")  
  
See log for complete Python traceback.  
  
Exception in thread Thread-135 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 285, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 132, in run  
reason = json.loads(e.body)['description']  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  




OpenGL version: 3.3.0 - Build 31.0.101.2121
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G7 Notebook PC
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 34,122,080,256
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    PyYAML: 6.0.2
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 7 months ago

Cc: pett added
Component: Unassigned → Web Services
Owner: set to Zach Pearson
Platform: → all
Priority: normal → major
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Web services down

'rq info' reports zero workers.

Reported by Emilia Grzesiak

comment:2 by pett, 7 months ago

Cc: julio.bonilla@… added

comment:3 by Zach Pearson, 7 months ago

Resolution: → fixed
Status: assigned → closed

They should be back up now, sorry for the inconvenience!

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