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Opened 2 years ago
Closed 2 years ago
#9429 closed defect (fixed)
BlastProtein failed: 'bytes' object has no attribute 'items'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | high | Milestone: | 1.7 |
| Component: | Web Services | Version: | |
| Keywords: | Cc: | Elaine Meng, Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-73-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.pdb format
> pdb
Summary of feedback from opening
/home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 45
LYS A 56 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 64 ASP A 77 1
14
Start residue of secondary structure not found: HELIX 3 3 SER A 86 HIS A 113 1
28
Start residue of secondary structure not found: HELIX 4 4 PRO A 121 ARG A 131
1 11
Start residue of secondary structure not found: HELIX 5 5 ILE B 26 GLY B 28 1
3
32 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (260 )
Cannot find LINK/SSBOND residue CYS (263 )
Cannot find LINK/SSBOND residue CYS (283 )
Cannot find LINK/SSBOND residue CYS (286 )
Cannot find LINK/SSBOND residue ASN (53 )
27 messages similar to the above omitted
6tda_k_missing.pdb title:
Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome [more
info...]
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
> toolshed show
> ui tool show "Modeller Comparative"
No alignments chosen for modeling
> open /home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
Summary of feedback from opening
/home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
---
notes | Alignment identifier is 6tda_k_missing.afasta
Associated 6tda_k_missing.pdb chain K to 6tda_k_missing.pdb (#0) chain K/1-426
with 0 mismatches
Opened 1 sequences from 6tda_k_missing.afasta
> blastprotein 6tda_k_missing.afasta:1 database nr cutoff 1e-3 matrix BLOSUM62
> maxSeqs 100 version 1 name bp1
Webservices job id: 5MRMXDL6HUF5SI83
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> blastprotein database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp2
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp3
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> hide #!1 models
> show #!1 models
> select add #1
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> blastprotein database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp4
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp5
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein /K database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> 1 name bp6
Webservices job id: 9LPRWFOPL48HXMYQ
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
Cannot run BLAST without some kind of sequence.
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp7
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> select subtract #1
Nothing selected
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp8
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp9
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> view #1 clip false
> log metadata #1
Metadata for 6tda_k_missing.pdb #1
---
Title | Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome
Citation | Structure of swi/SNF chromatin remodeller RSC bound to anucleosome.
PMID: 32188943
Gene sources | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Experimental method | Electron microscopy
Resolution | 15.00Å
> log chains #1
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
> view #1 clip false
> show #!1 target m
> hide #!1 target m
[Repeated 1 time(s)]
> show #!1 target m
> blastprotein
> >6tda_k_missing.pdb(#0)chainK/1-426MSHQNQLIPQAYISNFHNRLTNEDDGIPIFTMAQQTRQHKRAKVVNYAEYDNDLFDEFNMNGSNFNNADTHYKDNAVSHENTPALTNGVTMDGSEYNVLENMNGADSIISNNKYDAGSNMVVESLSGLNSNNNASNGPSNKAQAQDIGNAVLPDLQDQHHNPFNILRYPKIRDTFINGKVVSPYRLNTDQETKANANSGEAIMIPITLDIEHMGHTIKDQFLWNYNDDSISPEEFASIYCKDLDMTSATLQTQIANIIKEQLKDLENIAATEIMSDLHVIINLTCNLQDRFFEDNFQWNLNDKSLTPERFATSIVQDLGLTREFIPLISQSLHETILKIKKDWVDGHLIQDHVPNDAAFGYLSGIRLDIDELGSNWCPRVEILTKEEIQKREIEKERNLRRLKRETDRLSRRGRRRLDDLETTMRM
> database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp10
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein
> MSHQNQLIPQAYISNFHNRLTNEDDGIPIFTMAQQTRQHKRAKVVNYAEYDNDLFDEFNMNGSNFNNADTHYKDNAVSHENTPALTNGVTMDGSEYNVLENMNGADSIISNNKYDAGSNMVVESLSGLNSNNNASNGPSNKAQAQDIGNAVLPDLQDQHHNPFNILRYPKIRDTFINGKVVSPYRLNTDQETKANANSGEAIMIPITLDIEHMGHTIKDQFLWNYNDDSISPEEFASIYCKDLDMTSATLQTQIANIIKEQLKDLENIAATEIMSDLHVIINLTCNLQDRFFEDNFQWNLNDKSLTPERFATSIVQDLGLTREFIPLISQSLHETILKIKKDWVDGHLIQDHVPNDAAFGYLSGIRLDIDELGSNWCPRVEILTKEEIQKREIEKERNLRRLKRETDRLSRRGRRRLDDLETTMRM
> database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp11
Webservices job id: MXYYR1508U8YY5NF
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> open help:user/tools/blastprotein.html
Opened help:user/tools/blastprotein.html
> blastprotein
> MSHQNQLIPQAYISNFHNRLTNEDDGIPIFTMAQQTRQHKRAKVVNYAEYDNDLFDEFNMNGSNFNNADTHYKDNAVSHENTPALTNGVTMDGSEYNVLENMNGADSIISNNKYDAGSNMVVESLSGLNSNNNASNGPSNKAQAQDIGNAVLPDLQDQHHNPFNILRYPKIRDTFINGKVVSPYRLNTDQETKANANSGEAIMIPITLDIEHMGHTIKDQFLWNYNDDSISPEEFASIYCKDLDMTSATLQTQIANIIKEQLKDLENIAATEIMSDLHVIINLTCNLQDRFFEDNFQWNLNDKSLTPERFATSIVQDLGLTREFIPLISQSLHETILKIKKDWVDGHLIQDHVPNDAAFGYLSGIRLDIDELGSNWCPRVEILTKEEIQKREIEKERNLRRLKRETDRLSRRGRRRLDDLETTMRM
> database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp12
Webservices job id: EO2G9WMWBXBLEJTS
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
Cannot run BLAST without some kind of sequence.
> view #1 clip false
> show #!1 target m
> select add #1
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> blastprotein /K database pdb cutoff 1e-6 matrix BLOSUM62 maxSeqs 100 version
> 1 name bp13
Webservices job id: BMCI9T0ZEN72GNB5
Alignment identifier is bp13 [1]
Associated 6tda_k_missing.pdb chain K to 6K15_G with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp13 [1]
> open pdb:6K15
Summary of feedback from opening 6K15 fetched from pdb
---
notes | Fetching compressed mmCIF 6k15 from
http://files.rcsb.org/download/6k15.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
6k15 title:
RSC substrate-recruitment module [more info...]
Chain information for 6k15 #2
---
Chain | Description | UniProt
A | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
C | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
D H | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST 1-557
E | High temperature lethal protein 1 | HTL1_YEAST 1-78
F | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
G | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
I | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
J | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
K | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
L | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
M | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
X | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
Non-standard residues in 6k15 #2
---
ZN — zinc ion
Associated 6k15 chain G to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6k15 chain G to 6K15_G with 0 mismatches
> matchmaker #2/G to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6k15, chain G (#2), sequence
alignment score = 1804.7
RMSD between 174 pruned atom pairs is 0.781 angstroms; (across all 209 pairs:
2.544)
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: ATZ6RV3PIJ9L8L58
Modeller job (ID ATZ6RV3PIJ9L8L58) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 21 Jul 2023 21:48:54
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '60', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file "}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '#1K.B99990001.pdb: (400)\nReason: Bad Request\nHTTP response
headers: HTTPHeaderDict({\'Date\': \'Fri, 21 Jul 2023 21:48:54 GMT\',
\'Server\': \'Apache\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'60\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file "}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: KF03RBOSXN28Y0ZY
Modeller job (ID KF03RBOSXN28Y0ZY) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 21 Jul 2023 21:53:17
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '60', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file "}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '#1K.B99990001.pdb: (400)\nReason: Bad Request\nHTTP response
headers: HTTPHeaderDict({\'Date\': \'Fri, 21 Jul 2023 21:53:17 GMT\',
\'Server\': \'Apache\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'60\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file "}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
23379 atoms, 23808 bonds, 29 pseudobonds, 2891 residues, 5 models selected
> select subtract #2
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select add #2
23379 atoms, 23808 bonds, 29 pseudobonds, 2891 residues, 5 models selected
> select subtract #2
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
21486 atoms, 21882 bonds, 27 pseudobonds, 2656 residues, 3 models selected
> show (#!2 & sel) target ab
> cartoon hide (#!2 & sel)
> select subtract #2
Nothing selected
> hide #!2 models
> select add #1
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> ui tool show "Modeller Comparative"
> show #!2 models
> hide #!2 models
> modeller comparative "bp13 [1]:1" numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: 15L86E7ISZ5GA5Q0
Modeller job (ID 15L86E7ISZ5GA5Q0) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 21 Jul 2023 21:57:40
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '60', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file "}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '#1K.B99990001.pdb: (400)\nReason: Bad Request\nHTTP response
headers: HTTPHeaderDict({\'Date\': \'Fri, 21 Jul 2023 21:57:40 GMT\',
\'Server\': \'Apache\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'60\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file "}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
RuntimeError: Could not find Modeller out PDB #1K.B99990001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
> open pdb:6V8O
Summary of feedback from opening 6V8O fetched from pdb
---
note | Fetching compressed mmCIF 6v8o from
http://files.rcsb.org/download/6v8o.cif
6v8o title:
RSC core [more info...]
Chain information for 6v8o #3
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
Non-standard residues in 6v8o #3
---
ZN — zinc ion
Associated 6v8o chain Q to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 7 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 2 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 3 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 4 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 5 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain Q to 6K15_G with 0 mismatches
Associated 6v8o chain 7 to #1/K with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to #1/K with 0 mismatches
Associated 6v8o chain 4 to #1/K with 0 mismatches
Associated 6v8o chain 5 to #1/K with 0 mismatches
> matchmaker #3/Q to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6v8o, chain Q (#3), sequence
alignment score = 1814.9
RMSD between 177 pruned atom pairs is 0.695 angstroms; (across all 211 pairs:
2.510)
> open pdb:6V8O
6v8o title:
RSC core [more info...]
Chain information for 6v8o #4
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
Non-standard residues in 6v8o #4
---
ZN — zinc ion
Associated 6v8o chain Q to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 7 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 2 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 3 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 4 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 5 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain Q to 6K15_G with 0 mismatches
Associated 6v8o chain 7 to #1/K with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to #1/K with 0 mismatches
Associated 6v8o chain 4 to #1/K with 0 mismatches
Associated 6v8o chain 5 to #1/K with 0 mismatches
> matchmaker #4/Q to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6v8o, chain Q (#4), sequence
alignment score = 1814.9
RMSD between 177 pruned atom pairs is 0.695 angstroms; (across all 211 pairs:
2.510)
> open pdb:6KAG
Summary of feedback from opening 6KAG fetched from pdb
---
note | Fetching compressed mmCIF 6kag from
http://files.rcsb.org/download/6kag.cif
6kag title:
Crystal structure of the SMARCB1/SMARCC2 subcomplex [more info...]
Chain information for 6kag #5
---
Chain | Description | UniProt
A | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily B member 1 | SNF5_HUMAN 169-385
B C | SWI/SNF complex subunit SMARCC2 | SMRC2_HUMAN 325-518
> matchmaker #5/A to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6kag, chain A (#5), sequence
alignment score = 350.1
RMSD between 60 pruned atom pairs is 1.085 angstroms; (across all 156 pairs:
17.526)
> open pdb:6KAG
6kag title:
Crystal structure of the SMARCB1/SMARCC2 subcomplex [more info...]
Chain information for 6kag #6
---
Chain | Description | UniProt
A | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily B member 1 | SNF5_HUMAN 169-385
B C | SWI/SNF complex subunit SMARCC2 | SMRC2_HUMAN 325-518
> matchmaker #6/A to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6kag, chain A (#6), sequence
alignment score = 350.1
RMSD between 60 pruned atom pairs is 1.085 angstroms; (across all 156 pairs:
17.526)
> close #4
> close #5
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> style sel stick
Changed 1893 atom styles
> select subtract #1
Nothing selected
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> style sel stick
Changed 25103 atom styles
> style sel sphere
Changed 25103 atom styles
> style sel ball
Changed 25103 atom styles
> show sel cartoons
[Repeated 2 time(s)]
> hide sel cartoons
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 25103 atom styles
> style sel stick
Changed 25103 atom styles
> style sel stick
Changed 25103 atom styles
> style sel ball
Changed 25103 atom styles
> style sel ball
Changed 25103 atom styles
> style sel sphere
Changed 25103 atom styles
> style sel stick
Changed 25103 atom styles
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show sel cartoons
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!1-2 atoms
> show #!1-2 cartoons
[Repeated 1 time(s)]
> style #!1-2 stick
Changed 23379 atom styles
> hide #!1-2 cartoons
[Repeated 1 time(s)]
> show #!1-2 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1-2 cartoons
[Repeated 1 time(s)]
> show #!1-2 cartoons
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 atoms
> show #!2 models
> select add #2
46589 atoms, 47426 bonds, 48 pseudobonds, 5813 residues, 6 models selected
> select subtract #3
21486 atoms, 21882 bonds, 27 pseudobonds, 2656 residues, 3 models selected
> hide sel atoms
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> ui tool show "Modeller Comparative"
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> hide #3.1 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> select subtract #3.1
25103 atoms, 25544 bonds, 17 pseudobonds, 3157 residues, 2 models selected
> select subtract #3.2
25103 atoms, 25544 bonds, 3157 residues, 1 model selected
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> select subtract #3.1
25103 atoms, 25544 bonds, 17 pseudobonds, 3157 residues, 2 models selected
> select subtract #3.2
25103 atoms, 25544 bonds, 3157 residues, 1 model selected
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #!3 models
> show #3.2 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: 0J46I4K6QGWG1MRX
Modeller job (ID 0J46I4K6QGWG1MRX) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 80, in
append
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
_modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence:
? 3386 1
> show #3.1 models
> movie record
> turn y 2 180
> wait 180
> movie encode /home/wenhan/Desktop/movie1.mp4
Movie saved to /home/wenhan/Desktop/movie1.mp4
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: IGW3A08EVBGJWX0P
Modeller job (ID IGW3A08EVBGJWX0P) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 80, in
append
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
_modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence:
? 3386 1
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> select add #1
26996 atoms, 27470 bonds, 23 pseudobonds, 3392 residues, 5 models selected
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: BXUCVE9ZN4ZF3JJR
Modeller job (ID BXUCVE9ZN4ZF3JJR) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 80, in
append
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
_modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence:
? 3386 1
> select subtract #3
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
Alignment identifier is bp13 [2]
Associated 6tda_k_missing.pdb chain K to #1/K with 0 mismatches
Associated 6k15 chain G to #1/K with 0 mismatches
Associated 6v8o chain Q to #1/K with 0 mismatches
Associated 6v8o chain 7 to 6KAG_A with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to 6KAG_A with 0 mismatches
Associated 6v8o chain 4 to 6KAG_A with 0 mismatches
Associated 6v8o chain 5 to 6KAG_A with 0 mismatches
Associated 6kag chain A to 6KAG_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp13 [2]
> ui tool show "Modeller Comparative"
> modeller comparative "bp13 [1]:1" numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: C19WBQWFED2FIW3H
Modeller job (ID C19WBQWFED2FIW3H) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 80, in
append
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
_modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence:
? 3386 1
> ui tool show "Model Loops"
> modeller refine "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> modeller refine "bp13 [2]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [2]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> select add #3
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> select add #1
26996 atoms, 27470 bonds, 23 pseudobonds, 3392 residues, 5 models selected
> hide #!3 models
> show #!2 models
> select subtract #3
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select add #2
23379 atoms, 23808 bonds, 29 pseudobonds, 2891 residues, 5 models selected
> modeller refine "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> modeller refine 6tda_k_missing.afasta:1:internal-missing numModels 5 fast
> false adjacentFlexible 1 protocol standard
Webservices job id: S6QD2JKBEH8KQM0S
Webservices job id: 99ORM93UDH0VA2Z8
Modeller job (ID 99ORM93UDH0VA2Z8) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 97, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and
pdb files are different: 2655 511 For alignment entry: 1 6k15_2
Webservices job id: 69DOZ3ZVRYXUYXFO
Modeller job (ID 69DOZ3ZVRYXUYXFO) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 95, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 80, in
append
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
_modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence:
? 3133 1
> close #3
> close #6
> ui tool show "Model Loops"
[Repeated 1 time(s)]
> modeller refine "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> select subtract #2
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> close #2
Modeller job (ID S6QD2JKBEH8KQM0S) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 21 Jul 2023 22:14:27
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '80', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file 6tda_k_missing.pdb_("}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb: (400)\nReason:
Bad Request\nHTTP response headers: HTTPHeaderDict({\'Date\': \'Fri, 21 Jul
2023 22:14:27 GMT\', \'Server\': \'Apache\', \'Strict-Transport-Security\':
\'max-age=63072000; includeSubdomains; preload\', \'Content-Length\': \'80\',
\'vary\': \'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file 6tda_k_missing.pdb_("}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB
6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb on server
RuntimeError: Could not find Modeller out PDB
6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
> open pdb:6V8O
6v8o title:
RSC core [more info...]
Chain information for 6v8o #2
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
Non-standard residues in 6v8o #2
---
ZN — zinc ion
Associated 6v8o chain Q to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 7 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 2 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 3 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 4 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain 5 to 6tda_k_missing.pdb (#0) chain K/1-426 with 0
mismatches
Associated 6v8o chain Q to 6K15_G with 0 mismatches
Associated 6v8o chain 7 to #1/K with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to #1/K with 0 mismatches
Associated 6v8o chain 4 to #1/K with 0 mismatches
Associated 6v8o chain 5 to #1/K with 0 mismatches
> matchmaker #2/Q to #1/K
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 6tda_k_missing.pdb, chain K (#1) with 6v8o, chain Q (#2), sequence
alignment score = 1814.9
RMSD between 177 pruned atom pairs is 0.695 angstroms; (across all 211 pairs:
2.510)
> show cartoons
> hide atoms
> ui tool show "Model Loops"
> modeller refine "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [1]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> view clip false
[Repeated 1 time(s)]
> log metadata #1
Metadata for 6tda_k_missing.pdb #1
---
Title | Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome
Citation | Structure of swi/SNF chromatin remodeller RSC bound to anucleosome.
PMID: 32188943
Gene sources | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Experimental method | Electron microscopy
Resolution | 15.00Å
> log chains #1
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
> log metadata #2
Metadata for 6v8o #2
---
Title | RSC core
Citation | Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A.,
Ranish, J., Nogales, E. (2019). Architecture of the chromatin remodeler RSC
and insights into its nucleosome engagement. Elife, 8. PMID: 31886770. DOI:
10.7554/eLife.54449
Non-standard residue | ZN — zinc ion
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)
CryoEM Map | EMDB 21107 — open map
Experimental method | Electron microscopy
Resolution | 3.07Å
> log chains #2
Chain information for 6v8o #2
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
> select add #2
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> log metadata #1
Metadata for 6tda_k_missing.pdb #1
---
Title | Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome
Citation | Structure of swi/SNF chromatin remodeller RSC bound to anucleosome.
PMID: 32188943
Gene sources | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Experimental method | Electron microscopy
Resolution | 15.00Å
> log chains #1
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
> log metadata #2
Metadata for 6v8o #2
---
Title | RSC core
Citation | Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A.,
Ranish, J., Nogales, E. (2019). Architecture of the chromatin remodeler RSC
and insights into its nucleosome engagement. Elife, 8. PMID: 31886770. DOI:
10.7554/eLife.54449
Non-standard residue | ZN — zinc ion
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)
CryoEM Map | EMDB 21107 — open map
Experimental method | Electron microscopy
Resolution | 3.07Å
> log chains #2
Chain information for 6v8o #2
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
> log metadata #1
Metadata for 6tda_k_missing.pdb #1
---
Title | Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome
Citation | Structure of swi/SNF chromatin remodeller RSC bound to anucleosome.
PMID: 32188943
Gene sources | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Experimental method | Electron microscopy
Resolution | 15.00Å
> log chains #1
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
> log metadata #2
Metadata for 6v8o #2
---
Title | RSC core
Citation | Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A.,
Ranish, J., Nogales, E. (2019). Architecture of the chromatin remodeler RSC
and insights into its nucleosome engagement. Elife, 8. PMID: 31886770. DOI:
10.7554/eLife.54449
Non-standard residue | ZN — zinc ion
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)
CryoEM Map | EMDB 21107 — open map
Experimental method | Electron microscopy
Resolution | 3.07Å
> log chains #2
Chain information for 6v8o #2
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
Alignment identifier is bp13 [3]
Associated 6tda_k_missing.pdb chain K to 6V8O_Q with 0 mismatches
Associated 6v8o chain Q to 6V8O_Q with 0 mismatches
Associated 6v8o chain 7 to #1/K with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to #1/K with 0 mismatches
Associated 6v8o chain 4 to #1/K with 0 mismatches
Associated 6v8o chain 5 to #1/K with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp13 [3]
> ui tool show "Model Loops"
> modeller refine "bp13 [3]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [3]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> modeller refine "bp13 [3]:2:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [3]:2:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> modeller refine "bp13 [3]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [3]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
Alignment identifier is bp13 [4]
Associated 6tda_k_missing.pdb chain K to 6V8O_Q with 0 mismatches
Associated 6v8o chain Q to 6V8O_Q with 0 mismatches
Associated 6v8o chain 7 to #1/K with 0 mismatches
Associated 6v8o chain 2 to #1/K with 0 mismatches
Associated 6v8o chain 3 to #1/K with 0 mismatches
Associated 6v8o chain 4 to #1/K with 0 mismatches
Associated 6v8o chain 5 to #1/K with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp13 [4]
> blastprotein #1/K database pdb cutoff 1e-6 matrix BLOSUM62 maxSeqs 100
> version 1 name bp14
Webservices job id: XCD7FMO7CTABBQ20
> log metadata #2
Metadata for 6v8o #2
---
Title | RSC core
Citation | Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A.,
Ranish, J., Nogales, E. (2019). Architecture of the chromatin remodeler RSC
and insights into its nucleosome engagement. Elife, 8. PMID: 31886770. DOI:
10.7554/eLife.54449
Non-standard residue | ZN — zinc ion
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)
CryoEM Map | EMDB 21107 — open map
Experimental method | Electron microscopy
Resolution | 3.07Å
> log chains #2
Chain information for 6v8o #2
---
Chain | Description | UniProt
2 | Unknown protein |
3 4 | Unknown Protein |
5 | Unknown protein |
6 | Unknown Protein |
7 | Unknown Protein |
C | High temperature lethal protein 1 | HTL1_YEAST 1-78
D | Chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST 1-180
E | Chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST 1-435
F | Chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST 1-889
G | Chromatin structure-remodeling complex protein RSC3 | RSC3_YEAST 1-885
H | Chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST 1-625
I J K L | Chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
1-557
M | Chromatin structure-remodeling complex protein RSC6 | RSC6_YEAST 1-483
N | Chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST 1-581
O | Chromatin structure-remodeling complex protein RSC58 | RSC58_YEAST 1-502
Q | Chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
R | Nuclear protein STH1/NPS1 | STH1_YEAST 1-1359
S | Chromatin structure-remodeling complex protein RSC30 | RSC30_YEAST 1-883
> modeller refine "bp13 [4]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [4]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #!2 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #!2 models
> modeller refine "bp13 [4]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
> modeller loops "bp13 [4]:1:internal-missing" numModels 5 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: No sequences match 'bp13'
> show target m
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> show target m
> select add #2
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
25103 atoms, 25544 bonds, 21 pseudobonds, 3157 residues, 3 models selected
> ui tool show "Model Loops"
> close #2
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> close
> open /home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
> format fasta
Summary of feedback from opening
/home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
---
note | Alignment identifier is 6tda_k_missing.afasta
Opened 1 sequences from 6tda_k_missing.afasta
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence. Please open a model and select
a chain, or input sequences or a UniProt ID.
> open /home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
> format fasta
Summary of feedback from opening
/home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.afasta
---
notes | Destroying pre-existing alignment with identifier
6tda_k_missing.afasta
Alignment identifier is 6tda_k_missing.afasta
Opened 1 sequences from 6tda_k_missing.afasta
> show # target m
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> open /home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.pdb
Summary of feedback from opening
/home/wenhan/Desktop/HOUFANG/protonation/6tda/6tda_k_missing.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 45
LYS A 56 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 64 ASP A 77 1
14
Start residue of secondary structure not found: HELIX 3 3 SER A 86 HIS A 113 1
28
Start residue of secondary structure not found: HELIX 4 4 PRO A 121 ARG A 131
1 11
Start residue of secondary structure not found: HELIX 5 5 ILE B 26 GLY B 28 1
3
32 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (260 )
Cannot find LINK/SSBOND residue CYS (263 )
Cannot find LINK/SSBOND residue CYS (283 )
Cannot find LINK/SSBOND residue CYS (286 )
Cannot find LINK/SSBOND residue ASN (53 )
27 messages similar to the above omitted
6tda_k_missing.pdb title:
Structure of swi/SNF chromatin remodeler RSC bound to A nucleosome [more
info...]
Chain information for 6tda_k_missing.pdb #1
---
Chain | Description | UniProt
K | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST 1-426
Associated 6tda_k_missing.pdb chain K to 6tda_k_missing.pdb (#0) chain K/1-426
with 0 mismatches
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp15
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> select add #1
1893 atoms, 1926 bonds, 2 pseudobonds, 235 residues, 2 models selected
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp16
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp17
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1
> name bp18
Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence
> blastprotein /K database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> 1 name bp19
Webservices job id: A88GS8P2SLZ22YSZ
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> ui tool show "Model Loops"
> modeller refine 6tda_k_missing.afasta:1:internal-missing numModels 5 fast
> false adjacentFlexible 1 protocol standard
Webservices job id: WHSUYDLYQ7EYOKJK
> ui tool show "Model Loops"
Modeller job (ID WHSUYDLYQ7EYOKJK) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 21 Jul 2023 22:25:04
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '80', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file 6tda_k_missing.pdb_("}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb: (400)\nReason:
Bad Request\nHTTP response headers: HTTPHeaderDict({\'Date\': \'Fri, 21 Jul
2023 22:25:04 GMT\', \'Server\': \'Apache\', \'Strict-Transport-Security\':
\'max-age=63072000; includeSubdomains; preload\', \'Content-Length\': \'80\',
\'vary\': \'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file 6tda_k_missing.pdb_("}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB
6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb on server
RuntimeError: Could not find Modeller out PDB
6tda_k_missing.pdb_(#0)_chain_K1-426.BL00010001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) Graphics (RKL GT1)
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8940
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
Cache Size: 16384 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 7.7Gi 654Mi 850Mi 6.9Gi 6.4Gi
Swap: 47Gi 746Mi 46Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4c8a] (rev 04)
DeviceName: Onboard - Video
Subsystem: Dell Device [1028:09c5]
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (7)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Web Services |
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → high |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → BlastProtein failed: 'bytes' object has no attribute 'items' |
comment:2 by , 2 years ago
| Milestone: | → 1.7 |
|---|
comment:3 by , 2 years ago
Blast works from my machine. Could have been a transient error -- e.g. webservices failover.
Inspecting /var/tmp/job_id, the correct files are all there. The error probably comes from the hash in the filename since webservices complains it can't find "6tda_k_missing.pdb_("
comment:4 by , 2 years ago
| Cc: | added |
|---|
This continues to fail for me. I am using last night's daily build that was automatically installed on sussex.
comment:6 by , 2 years ago
From the logs: RuntimeError: BLAST Database error: Could not find volume or alias file (nr.74) referenced in alias file (/wynton/group/ferrin/databases/mol/blast/db_current/nr
comment:7 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Repeat with:
open 6tda
blastprotein /K database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp6
Modeller was also failing, but it could be the same root cause as what's making Blast fail.