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Opened 5 months ago
Closed 5 months ago
#18006 closed defect (duplicate)
Web services down
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Infrastructure | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-139-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
seq align #1,#2 error
Alignment identifier is 2 Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align return session.alignments.new_alignment(realigned, None, name=title) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 253, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 91, in __init__ raise ValueError("Cannot create alignment of zero sequences") See log for complete Python traceback. Exception in thread Thread-255 (_run_function): Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/tasks.py", line 300, in _run_function func(*args, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/webservices/cxservices_job.py", line 148, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/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)
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /mnt/sdb2/kevin3/unrelated/rhamnose/st1_25/data/1116.cxs format session
Log from Mon Jun 16 15:13:24 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /mnt/sdb2/kevin3/unrelated/rhamnose/st1_25/data/fold_p17_16_model_0.cif
Chain information for fold_p17_16_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open
> /mnt/sdb2/kevin3/unrelated/rhamnose/st1_25/data/fold_st25_16_model_0.cif
Chain information for fold_st25_16_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> sequence align #1/A,#2/A
Alignment identifier is 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-77 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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)
> sequence align #1/A,#2/A
Alignment identifier is 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-154 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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
2663 atoms, 2719 bonds, 326 residues, 1 model selected
> select add #2
5332 atoms, 5447 bonds, 652 residues, 2 models selected
> sequence align #1/A,#2/A
Alignment identifier is 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-233 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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)
> toolshed show
> sequence align #1/A,#2/A
Alignment identifier is 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-310 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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)
> save /mnt/sdb2/kevin3/unrelated/rhamnose/st1_25/data/1116.cxs
——— End of log from Mon Jun 16 15:13:24 2025 ———
opened ChimeraX session
> sequence align #1/A:1,#2/A:1
Alignment identifier is 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-78 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 subtract #1
2669 atoms, 2728 bonds, 326 residues, 1 model selected
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
No 'to' model specified
> matchmaker #2 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 fold_p17_16_model_0.cif, chain A (#1) with
fold_st25_16_model_0.cif, chain A (#2), sequence alignment score = 1443.3
RMSD between 323 pruned atom pairs is 0.581 angstroms; (across all 326 pairs:
0.705)
> matchmaker #2 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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_p17_16_model_0.cif, chain A (#1) with
fold_st25_16_model_0.cif, chain A (#2), sequence alignment score = 1443.3
RMSD between 323 pruned atom pairs is 0.581 angstroms; (across all 326 pairs:
0.705)
> matchmaker #2 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 fold_p17_16_model_0.cif, chain A (#1) with
fold_st25_16_model_0.cif, chain A (#2), sequence alignment score = 1443.3
RMSD between 323 pruned atom pairs is 0.581 angstroms; (across all 326 pairs:
0.705)
> matchmaker #2 to #1 showAlignment true
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_p17_16_model_0.cif, chain A (#1) with
fold_st25_16_model_0.cif, chain A (#2), sequence alignment score = 1443.3
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: fold_p17_16_model_0.cif #1/A,
fold_st25_16_model_0.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 323 pruned atom pairs is 0.581 angstroms; (across all 326 pairs:
0.705)
> select #1/A:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:172-173 #2/A:172-173
26 atoms, 24 bonds, 4 residues, 2 models selected
MatchMaker Alignment [ID: 1] region fold_p17_16_model_0.cif, chain
A..fold_st25_16_model_0.cif, chain A [172-173] RMSD: 3.257
> matchmaker #2 to #1 showAlignment true
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_p17_16_model_0.cif, chain A (#1) with
fold_st25_16_model_0.cif, chain A (#2), sequence alignment score = 1443.3
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: fold_p17_16_model_0.cif #1/A,
fold_st25_16_model_0.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 323 pruned atom pairs is 0.581 angstroms; (across all 326 pairs:
0.705)
> sequence align #1,#2
Alignment identifier is 2
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-178 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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)
> sequence align #1 #2
Alignment identifier is 2
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 481, in seqalign_align
return session.alignments.new_alignment(realigned, None, name=title)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 91, in __init__
raise ValueError("Cannot create alignment of zero sequences")
See log for complete Python traceback.
Exception in thread Thread-255 (_run_function):
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038, in
_bootstrap_inner
self.run()
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 148, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/__init__.py", line 346, in
loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/json/decoder.py", line 337, in
decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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: 4.5 (Core Profile) Mesa 21.2.6
OpenGL renderer: llvmpipe (LLVM 12.0.0, 256 bits)
OpenGL vendor: Mesa/X.org
Python: 3.11.4
Locale: en_CA.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=MATE
WAYLAND_DISPLAY=no
DISPLAY=:1002
Manufacturer: HP
Model: HP Z8 G4 Workstation
OS: Linux Mint 20.2
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz
Cache Size: 25344 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 34Gi 49Gi 1.0Gi 41Gi 88Gi
Swap: 9Gi 4.6Gi 5.4Gi
Graphics:
2d:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: Hewlett-Packard Company TU104GL [Quadro RTX 4000] [103c:12a0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Infrastructure |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Web services down |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Report from yesterday before the web services were restored