Opened 16 months ago

Closed 13 months ago

#15704 closed defect (fixed)

BLAST databases missing

Reported by: 23036745r@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Web Services Version:
Keywords: Cc: Greg Couch, Scooter Morris
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> ~select

Nothing selected  
Log from Tue Jul 30 16:37:05 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/USER/OneDrive - The Hong Kong Polytechnic University/Lab
> Documents/Log book/Log Ubi/Ubi coot/Ubi with
> uq/RRS61_with_UQplaceholder.pdb"

Chain information for RRS61_with_UQplaceholder.pdb #1  
---  
Chain | Description  
A B C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J K | No description available  
  

> hide atoms

> show cartoons

> ui tool show "Blast Protein"

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C

Alignment identifier is 1  

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp1

Webservices job id: VG9FUD493YU3WEPD  
Alignment identifier is bp1 [1]  
Associated RRS61_with_UQplaceholder.pdb chain A to #1/A with 0 mismatches  
Associated RRS61_with_UQplaceholder.pdb chain B to #1/A with 0 mismatches  
Associated RRS61_with_UQplaceholder.pdb chain C to #1/A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> open pdb:4OBW

4obw title:  
crystal structure of yeast Coq5 in the SAM bound form [more info...]  
  
Chain information for 4obw #2  
---  
Chain | Description | UniProt  
A B C D | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | COQ5_YEAST 61-307  
  
Non-standard residues in 4obw #2  
---  
SAM — S-adenosylmethionine  
TAM — tris(hydroxyethyl)aminomethane  
  
4obw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 4obw chain A to 4OBX_A with 0 mismatches  
Associated 4obw chain D to 4OBX_A with 0 mismatches  
Associated 4obw chain C to 4OBX_A with 0 mismatches  
Associated 4obw chain B to 4OBX_A with 0 mismatches  

> matchmaker #2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 4OBW_A, chain A
(#2), sequence alignment score = 582.7  
RMSD between 141 pruned atom pairs is 0.905 angstroms; (across all 219 pairs:
3.373)  
  

> open pdb:4OBX

Summary of feedback from opening 4OBX fetched from pdb  
---  
note | Fetching compressed mmCIF 4obx from http://files.rcsb.org/download/4obx.cif  
  
4obx title:  
Crystal structure of yeast Coq5 in the apo form [more info...]  
  
Chain information for 4obx #3  
---  
Chain | Description | UniProt  
A B C D | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | COQ5_YEAST 61-307  
  
Non-standard residues in 4obx #3  
---  
TAM — tris(hydroxyethyl)aminomethane  
  
4obx mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 4obx chain A to 4OBX_A with 0 mismatches  
Associated 4obx chain D to 4OBX_A with 0 mismatches  
Associated 4obx chain C to 4OBX_A with 0 mismatches  
Associated 4obx chain B to 4OBX_A with 0 mismatches  

> matchmaker #3/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 4OBX_A, chain A
(#3), sequence alignment score = 588.1  
RMSD between 140 pruned atom pairs is 0.967 angstroms; (across all 220 pairs:
3.416)  
  

> open pdb:3DH0

Summary of feedback from opening 3DH0 fetched from pdb  
---  
note | Fetching compressed mmCIF 3dh0 from http://files.rcsb.org/download/3dh0.cif  
  
3dh0 title:  
Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus
[more info...]  
  
Chain information for 3dh0 #4  
---  
Chain | Description | UniProt  
A B | SAM dependent methyltransferase | O67440_AQUAE 4-211  
  
Non-standard residues in 3dh0 #4  
---  
SAM — S-adenosylmethionine  
  
3dh0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 3dh0 chain A to 3DH0_A with 0 mismatches  
Associated 3dh0 chain B to 3DH0_A with 0 mismatches  

> matchmaker #4/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 3DH0_A, chain A
(#4), sequence alignment score = 293.4  
RMSD between 97 pruned atom pairs is 1.168 angstroms; (across all 180 pairs:
5.419)  
  

> open pdb:1XXL

Summary of feedback from opening 1XXL fetched from pdb  
---  
notes | Fetching compressed mmCIF 1xxl from http://files.rcsb.org/download/1xxl.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
  
1xxl title:  
The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A
resolution [more info...]  
  
Chain information for 1xxl #5  
---  
Chain | Description | UniProt  
A B | YcgJ protein | O31474_BACSU 2-228  
  
Non-standard residues in 1xxl #5  
---  
SO4 — sulfate ion  
  
1xxl mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
Associated 1xxl chain A to 2GLU_A with 1 mismatch  
Associated 1xxl chain B to 2GLU_A with 1 mismatch  

> matchmaker #5/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 1XXL_A, chain A
(#5), sequence alignment score = 279.3  
RMSD between 124 pruned atom pairs is 0.960 angstroms; (across all 190 pairs:
12.711)  
  

> open pdb:2GLU

Summary of feedback from opening 2GLU fetched from pdb  
---  
note | Fetching compressed mmCIF 2glu from http://files.rcsb.org/download/2glu.cif  
  
2glu title:  
The crystal structure of YcgJ protein from Bacillus subitilis [more info...]  
  
Chain information for 2glu #6  
---  
Chain | Description  
A B | ycgJ  
  
Non-standard residues in 2glu #6  
---  
SAM — S-adenosylmethionine  
SO4 — sulfate ion  
  
2glu mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
Associated 2glu chain A to 2GLU_A with 1 mismatch  
Associated 2glu chain B to 2GLU_A with 1 mismatch  

> matchmaker #6/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 2GLU_A, chain A
(#6), sequence alignment score = 265.9  
RMSD between 124 pruned atom pairs is 1.062 angstroms; (across all 169 pairs:
5.989)  
  

> open pdb:6UAK

Summary of feedback from opening 6UAK fetched from pdb  
---  
warning | Atom OE2 has no neighbors to form bonds with according to residue template for GLU /A:251  
note | Fetching compressed mmCIF 6uak from http://files.rcsb.org/download/6uak.cif  
  
6uak title:  
LahSb - C-terminal methyltransferase involved in RiPP biosynthesis [more
info...]  
  
Chain information for 6uak #7  
---  
Chain | Description | UniProt  
A | SAM dependent methyltransferase LahSB | A0A3D0LE54_9FIRM 4-306  
  
Non-standard residues in 6uak #7  
---  
SAH — S-adenosyl-L-homocysteine  
  
6uak mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Associated 6uak chain A to 6UAK_A with 0 mismatches  

> matchmaker #7/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 6UAK_A, chain A
(#7), sequence alignment score = 302.9  
RMSD between 91 pruned atom pairs is 1.138 angstroms; (across all 200 pairs:
10.323)  
  

> open pdb:1VL5

Summary of feedback from opening 1VL5 fetched from pdb  
---  
warning | Atom O has no neighbors to form bonds with according to residue template for GLU /A:100  
note | Fetching compressed mmCIF 1vl5 from http://files.rcsb.org/download/1vl5.cif  
  
1vl5 title:  
Crystal structure of A putative methyltransferase (BH2331) from bacillus
halodurans C-125 At 1.95 A resolution [more info...]  
  
Chain information for 1vl5 #8  
---  
Chain | Description | UniProt  
A B C D | unknown conserved protein BH2331 | Q9KAF6_BACHD 19-265  
  
1vl5 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 1vl5 chain A to 1VL5_A with 1 mismatch  
Associated 1vl5 chain B to 1VL5_A with 1 mismatch  
Associated 1vl5 chain C to 1VL5_A with 1 mismatch  
Associated 1vl5 chain D to 1VL5_A with 1 mismatch  

> matchmaker #8/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 1VL5_A, chain A
(#8), sequence alignment score = 287.3  
RMSD between 116 pruned atom pairs is 1.053 angstroms; (across all 173 pairs:
7.330)  
  

> open pdb:3MGG

Summary of feedback from opening 3MGG fetched from pdb  
---  
note | Fetching compressed mmCIF 3mgg from http://files.rcsb.org/download/3mgg.cif  
  
3mgg title:  
Crystal Structure of Methyl Transferase from Methanosarcina mazei [more
info...]  
  
Chain information for 3mgg #9  
---  
Chain | Description | UniProt  
A B | Methyltransferase | Q8PVL4_METMA 2-266  
  
Associated 3mgg chain A to 3MGG_A with 0 mismatches  
Associated 3mgg chain B to 3MGG_A with 0 mismatches  

> matchmaker #9/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 3MGG_A, chain A
(#9), sequence alignment score = 255.6  
RMSD between 91 pruned atom pairs is 1.126 angstroms; (across all 172 pairs:
8.307)  
  

> open pdb:6UV6

Summary of feedback from opening 6UV6 fetched from pdb  
---  
note | Fetching compressed mmCIF 6uv6 from http://files.rcsb.org/download/6uv6.cif  
  
6uv6 title:  
AtmM with bound rebeccamycin analogue [more info...]  
  
Chain information for 6uv6 #10  
---  
Chain | Description | UniProt  
A B C | D-glucose O-methyltransferase | Q0H2W9_9ACTN 1-268  
  
Non-standard residues in 6uv6 #10  
---  
BY9 — 12-beta-D-
glucopyranosyl-12,13-dihydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5,7(6H)-dione
(rebeccamycin analogue)  
SAH — S-adenosyl-L-homocysteine  
  
6uv6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
Associated 6uv6 chain A to 6UV6_A with 0 mismatches  
Associated 6uv6 chain B to 6UV6_A with 0 mismatches  
Associated 6uv6 chain C to 6UV6_A with 0 mismatches  

> matchmaker #10/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 6UV6_A, chain A
(#10), sequence alignment score = 299  
RMSD between 97 pruned atom pairs is 1.083 angstroms; (across all 206 pairs:
14.889)  
  

> hide #2-6,9-10#!7-8 target m

> close #2-6,9-10#7-8

> open pdb:3DH0

3dh0 title:  
Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus
[more info...]  
  
Chain information for 3dh0 #2  
---  
Chain | Description | UniProt  
A B | SAM dependent methyltransferase | O67440_AQUAE 4-211  
  
Non-standard residues in 3dh0 #2  
---  
SAM — S-adenosylmethionine  
  
3dh0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 3dh0 chain A to 3DH0_A with 0 mismatches  
Associated 3dh0 chain B to 3DH0_A with 0 mismatches  

> matchmaker #2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 3DH0_A, chain A
(#2), sequence alignment score = 293.4  
RMSD between 97 pruned atom pairs is 1.168 angstroms; (across all 180 pairs:
5.419)  
  

> close #2

> open pdb:3DH0

3dh0 title:  
Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus
[more info...]  
  
Chain information for 3dh0 #2  
---  
Chain | Description | UniProt  
A B | SAM dependent methyltransferase | O67440_AQUAE 4-211  
  
Non-standard residues in 3dh0 #2  
---  
SAM — S-adenosylmethionine  
  
3dh0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Associated 3dh0 chain A to 3DH0_A with 0 mismatches  
Associated 3dh0 chain B to 3DH0_A with 0 mismatches  

> matchmaker #2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 3DH0_A, chain A
(#2), sequence alignment score = 293.4  
RMSD between 97 pruned atom pairs is 1.168 angstroms; (across all 180 pairs:
5.419)  
  

> open O67440 fromDatabase uniprot associate #2/A,B

Summary of feedback from opening O67440 fetched from uniprot  
---  
notes | Fetching compressed O67440 UniProt info from https://www.uniprot.org/uniprot/O67440.xml  
Alignment identifier is O67440  
Associated 3DH0_A chain A to O67440 with 2 mismatches  
Associated 3DH0_A chain B to O67440 with 2 mismatches  
  
Opened UniProt O67440  

> select #2/A-B:36-145

1778 atoms, 1820 bonds, 220 residues, 1 model selected  

> select #2/A-B:36-145

1778 atoms, 1820 bonds, 220 residues, 1 model selected  

> ~select

Nothing selected  

> select #2/A-B:6,20,69,97,115

88 atoms, 78 bonds, 10 residues, 1 model selected  

> select #2/A-B:36-145

1778 atoms, 1820 bonds, 220 residues, 1 model selected  

> select #2/A-B:6,20,69,97,115

88 atoms, 78 bonds, 10 residues, 1 model selected  

> select #2/A-B:6,20,69,97,115

88 atoms, 78 bonds, 10 residues, 1 model selected  

> open pdb:6UAK

Summary of feedback from opening 6UAK fetched from pdb  
---  
warning | Atom OE2 has no neighbors to form bonds with according to residue template for GLU /A:251  
  
6uak title:  
LahSb - C-terminal methyltransferase involved in RiPP biosynthesis [more
info...]  
  
Chain information for 6uak #3  
---  
Chain | Description | UniProt  
A | SAM dependent methyltransferase LahSB | A0A3D0LE54_9FIRM 4-306  
  
Non-standard residues in 6uak #3  
---  
SAH — S-adenosyl-L-homocysteine  
  
6uak mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Associated 6uak chain A to 6UAK_A with 0 mismatches  

> matchmaker #3/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 6UAK_A, chain A
(#3), sequence alignment score = 302.9  
RMSD between 91 pruned atom pairs is 1.138 angstroms; (across all 200 pairs:
10.323)  
  

> open A0A3D0LE54 fromDatabase uniprot associate #3/A

Summary of feedback from opening A0A3D0LE54 fetched from uniprot  
---  
notes | Fetching compressed A0A3D0LE54 UniProt info from https://www.uniprot.org/uniprot/A0A3D0LE54.xml  
Alignment identifier is A0A3D0LE54  
Associated 6UAK_A chain A to A0A3D0LE54 with 6 mismatches  
  
Opened UniProt A0A3D0LE54  

> select #3/A:40-164

954 atoms, 972 bonds, 125 residues, 1 model selected  

> select #3/A:21,72,98-99,115

42 atoms, 39 bonds, 5 residues, 1 model selected  

> select #2/A-B:36-145

1778 atoms, 1820 bonds, 220 residues, 1 model selected  

> select #2/A-B:36-145

1778 atoms, 1820 bonds, 220 residues, 1 model selected  

> ~select

Nothing selected  

> select #2/A-B:6,20,69,97,115

88 atoms, 78 bonds, 10 residues, 1 model selected  

> open pdb:1VL5

Summary of feedback from opening 1VL5 fetched from pdb  
---  
warning | Atom O has no neighbors to form bonds with according to residue template for GLU /A:100  
  
1vl5 title:  
Crystal structure of A putative methyltransferase (BH2331) from bacillus
halodurans C-125 At 1.95 A resolution [more info...]  
  
Chain information for 1vl5 #4  
---  
Chain | Description | UniProt  
A B C D | unknown conserved protein BH2331 | Q9KAF6_BACHD 19-265  
  
1vl5 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 1vl5 chain A to 1VL5_A with 1 mismatch  
Associated 1vl5 chain B to 1VL5_A with 1 mismatch  
Associated 1vl5 chain C to 1VL5_A with 1 mismatch  
Associated 1vl5 chain D to 1VL5_A with 1 mismatch  

> matchmaker #4/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 1VL5_A, chain A
(#4), sequence alignment score = 287.3  
RMSD between 116 pruned atom pairs is 1.053 angstroms; (across all 173 pairs:
7.330)  
  

> select #4/A,B,C,D:19-265

7186 atoms, 7361 bonds, 2 pseudobonds, 906 residues, 2 models selected  

> open Q9KAF6 fromDatabase uniprot associate #4/A,B,C,D

Summary of feedback from opening Q9KAF6 fetched from uniprot  
---  
notes | Fetching compressed Q9KAF6 UniProt info from https://www.uniprot.org/uniprot/Q9KAF6.xml  
Alignment identifier is Q9KAF6  
Associated 1VL5_A chain A to Q9KAF6 with 14 mismatches  
Associated 1VL5_A chain B to Q9KAF6 with 14 mismatches  
Associated 1VL5_A chain C to Q9KAF6 with 14 mismatches  
Associated 1VL5_A chain D to Q9KAF6 with 14 mismatches  
  
Opened UniProt Q9KAF6  

> select #4/A-D:47-142

2757 atoms, 2824 bonds, 2 pseudobonds, 366 residues, 2 models selected  

> select #4/A-D:47-142

2757 atoms, 2824 bonds, 2 pseudobonds, 366 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #2/B

Alignment identifier is 1  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #4/A #4/B #4/C #4/D

Alignment identifier is 2  

> sequence chain #1/A #1/B #1/C

Alignment identifier is 3  

> open pdb:3MGG

3mgg title:  
Crystal Structure of Methyl Transferase from Methanosarcina mazei [more
info...]  
  
Chain information for 3mgg #5  
---  
Chain | Description | UniProt  
A B | Methyltransferase | Q8PVL4_METMA 2-266  
  
Associated 3mgg chain A to 3MGG_A with 0 mismatches  
Associated 3mgg chain B to 3MGG_A with 0 mismatches  

> matchmaker #5/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RRS61_with_UQplaceholder.pdb, chain A (#1) with 3MGG_A, chain A
(#5), sequence alignment score = 255.6  
RMSD between 91 pruned atom pairs is 1.126 angstroms; (across all 172 pairs:
8.307)  
  

> open Q8PVL4 fromDatabase uniprot associate #5/A,B

Summary of feedback from opening Q8PVL4 fetched from uniprot  
---  
notes | Fetching compressed Q8PVL4 UniProt info from https://www.uniprot.org/uniprot/Q8PVL4.xml  
Alignment identifier is Q8PVL4  
Associated 3MGG_A chain A to Q8PVL4 with 1 mismatch  
Associated 3MGG_A chain B to Q8PVL4 with 1 mismatch  
  
Opened UniProt Q8PVL4  

> select #5/A-B:36-142

1624 atoms, 1648 bonds, 214 residues, 1 model selected  

> select #5/A-B:36-142

1624 atoms, 1648 bonds, 214 residues, 1 model selected  

> sequence header bp1 [1] rmsd show

Should be one of 'consensus', 'conservation', or 'rmsd'  

> sequence header bp1 [1] consensus show

Should be one of 'consensus', 'conservation', or 'rmsd'  

> sequence header bp1 [1] consensus show

Should be one of 'consensus', 'conservation', or 'rmsd'  

> hide #5 models

> hide #!4 models

> hide #!3 models

> hide #2 models

> show #2 models

> select ::name="UQ8"

318 atoms, 318 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel red

> select clear

> save "C:/Users/USER/OneDrive - The Hong Kong Polytechnic University/Lab
> Documents/Log book/Log Ubi/Analysis/ChimeraX_BLAST&align/UbiE.cxs"

——— End of log from Tue Jul 30 16:37:05 2024 ———

opened ChimeraX session  

> close #2,5#3-4

> ui tool show "Blast Protein"

> blastprotein /D database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp2

Webservices job id: UTI21X9CTTF751Y5  
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  

> ui tool show "Show Sequence Viewer"

> sequence chain /D

Alignment identifier is 1/D  

> blastprotein 1/D:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp3

Webservices job id: H26KJ8MO4HEYGYQN  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

> blastprotein 1/D:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp4

Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence  

> blastprotein /D database uniref100 cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp5

Webservices job id: K2U0629YH8NAFA8B  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

> select clear

[Repeated 1 time(s)]

> select /A:33 /B:33 /C:33

15 atoms, 12 bonds, 3 residues, 1 model selected  

> select /A-C:32-33

36 atoms, 33 bonds, 6 residues, 1 model selected  

> select /A-C:32-33

36 atoms, 33 bonds, 6 residues, 1 model selected  

> blastprotein /D database uniref100 cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 1 name bp6

Webservices job id: OWMNR9INEU9SDEJ6  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

> blastprotein /D database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> 1 name bp7

Webservices job id: 8ITWQKBU2VA22KGD  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

>

Unknown command: sequence #1/D  

> ui tool show "Show Sequence Viewer"

> sequence chain /D

Alignment identifier is 1/D  

> select /D:1

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

> select /D

3026 atoms, 3100 bonds, 391 residues, 1 model selected  

> blastprotein
> MTNQPTEIAIVGGGMVGGALALGLAQHGFAVTVIEHAEPAPFVADSQPDVRISAISAASVSLLKGLGVWDAVQAMRCHPYRRLETWEWETAHVVFDAAELKLPLLGYMVENTVLQQALWQALEAHPKVTLRVPGSLIALHRHDDLQELELKGGEVIRAKLVIGADGANSQVRQMAGIGVHAWQYAQSCMLISVQCENDPGDSTWQQFTPDGPRAFLPLFDNWASLVWYDSPARIRQLQNMNMAQLQAEIAKHFPSRLGYVTPLAAGAFPLTRRHALQYVQPGLALVGDAAHTIHPLAGQGVNLGYRDVDALIDVLVNARSYGEAWASYPVLKRYQMRRMADNFIMQSGMDLFYAGFSNNLPPLRFMRNLGLMAAERAGVLKRQALKYALGL
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp8

Webservices job id: W8PDOV0I49IE5VH0  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

> blastprotein
> MTNQPTEIAIVGGGMVGGALALGLAQHGFAVTVIEHAEPAPFVADSQPDVRISAISAASVSLLKGLGVWDAVQAMRCHPYRRLETWEWETAHVVFDAAELKLPLLGYMVENTVLQQALWQALEAHPKVTLRVPGSLIALHRHDDLQELELKGGEVIRAKLVIGADGANSQVRQMAGIGVHAWQYAQSCMLISVQCENDPGDSTWQQFTPDGPRAFLPLFDNWASLVWYDSPARIRQLQNMNMAQLQAEIAKHFPSRLGYVTPLAAGAFPLTRRHALQYVQPGLALVGDAAHTIHPLAGQGVNLGYRDVDALIDVLVNARSYGEAWASYPVLKRYQMRRMADNFIMQSGMDLFYAGFSNNLPPLRFMRNLGLMAAERAGVLKRQALKYALGL
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version 1 name bp9

Webservices job id: 76OC7V2TA2BC9ONW  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  




OpenGL version: 3.3.0 - Build 31.0.101.5333
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_HK.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82XF
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,890,322,944
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

Change History (7)

comment:1 by Zach Pearson, 16 months ago

Cc: Greg Couch added
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned

PCS status on our server shows many service failures. We have scheduled downtime, but my email says it's tomorrow. 

  * web-Production_monitor_60000 on franklin 'error' (1): call=321, status='Timed Out', exitreason='Resource agent did not complete within 40s', last-rc-change='Wed Jul 31 06:09:26 2024', queued=0ms, exec=0ms
  * spoke-neo4j_monitor_15000 on crick 'error' (1): call=2117, status='Timed Out', exitreason='Resource agent did not complete within 15s', last-rc-change='Tue Jul 30 13:23:48 2024', queued=0ms, exec=0ms
  * web-SPOKE-Apache_monitor_10000 on crick 'error' (1): call=2119, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 13:23:53 2024', queued=0ms, exec=0ms
  * web-WebServices-Apache_monitor_10000 on crick 'error' (1): call=2087, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Sat Jul 27 20:31:45 2024', queued=0ms, exec=0ms
  * web-Preview-Apache_monitor_10000 on watson 'error' (1): call=10494, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 15:15:29 2024', queued=0ms, exec=0ms
  * web-WebServices-Test-Apache_monitor_10000 on watson 'error' (1): call=10474, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 13:23:54 2024', queued=0ms, exec=0ms
  * spokedev-neo4j_monitor_15000 on watson 'error' (1): call=10528, status='Timed Out', exitreason='Resource agent did not complete within 15s', last-rc-change='Tue Jul 30 13:23:48 2024', queued=0ms, exec=0ms
  * web-SPOKEdev-Apache_monitor_10000 on watson 'error' (1): call=10538, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 15:15:29 2024', queued=0ms, exec=0ms
  * web-CxToolshed-Apache_monitor_10000 on watson 'error' (1): call=10490, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 13:23:53 2024', queued=0ms, exec=0ms
  * web-SFLD-Apache_monitor_10000 on wilkins 'error' (1): call=9624, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 13:23:53 2024', queued=0ms, exec=0ms
  * spokebuild-neo4j_monitor_15000 on wilkins 'error' (1): call=9646, status='Timed Out', exitreason='Resource agent did not complete within 15s', last-rc-change='Tue Jul 30 13:23:48 2024', queued=0ms, exec=0ms
  * web-Mail_monitor_10000 on wilkins 'error' (1): call=9610, status='Timed Out', exitreason='Resource agent did not complete within 20s', last-rc-change='Tue Jul 30 13:24:19 2024', queued=0ms, exec=0ms

comment:2 by Zach Pearson, 16 months ago

Traceback from a job I just ran:

{
  "event": "[Job 5EYRG99NPJ7Q7TEP]: exception raised while executing (cxservices.task_runners.blast.run_job)\nTraceback (most recent call last):\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/worker.py\", line 1418, in perform_job\n    rv = job.perform()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/cxservices/worker.py\", line 39, in perform\n    result = super().perform()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/job.py\", line 1225, in perform\n    self._result = self._execute()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/job.py\", line 1262, in _execute\n    result = self.func(*self.args, **self.kwargs)\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/task_runners/blast.py\", line 75, in run_job\n    raise RuntimeError(job.stderr.decode(\"utf-8\"))\nRuntimeError: BLAST Database error: No alias or index file found for protein database [/databases/mol/AlphaFold/v2/alphafold.fasta] in search path [/var/lib/pacemaker/cores::]\n\n",
  "level": "error",
  "timestamp": "2024-07-31T17:34:31.340309Z"
}

comment:3 by Zach Pearson, 16 months ago

Summary: ChimeraX bug report submission → BLAST databases missing

In webservices we set the paths to the database prefixes as follows:

AlphaFoldDir = "/databases/mol/AlphaFold/v"
StdDbDir = "/databases/mol/blast/db_current"
UniRefDir = "/databases/mol/blast/db_uniref"
EsmfoldDir = "/databases/mol/ESMFold/v"

The AlphaFold and ESMFold directories are missing from /databases/mol/ and it looks to me like /databases/mol/blast/db_current is empty.

comment:4 by Zach Pearson, 16 months ago

I think you may have caught us during a database update; I will close this ticket when it completes and we will announce these in the future.

comment:5 by Eric Pettersen, 16 months ago

Cc: Scooter Morris added
Component: Unassigned → Web Services

comment:6 by Tom Goddard, 16 months ago

The BLAST databases were accidentally deleted. I restored the AlphaFold BLAST database from a backup. The PDB BLAST database and NR were recreated. The Uniref BLAST databases are still gone and Scooter said he is working on writing scripts to update those.

comment:7 by Zach Pearson, 13 months ago

Resolution: → fixed
Status: assigned → closed

This has been fixed for a while.

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