Blast: not enough values to unpack

[lp212@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Blasting protein sequence through PDB

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/luca/Downloads/AF-Q5T4T6-F1-model_v1.pdb

AF-Q5T4T6-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for synaptonemal complex protein 2-like (Q5T4T6)
[more info...]  
  
Chain information for AF-Q5T4T6-F1-model_v1.pdb #1  
---  
Chain | Description  
A | synaptonemal complex protein 2-like  
  

> select ::name="CYS"

54 atoms, 45 bonds, 9 residues, 1 model selected  

> show sel atoms

> color sel lime

> select clear

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/PDB_DEPO/pdb:cif/27.05.2021.pdb"

Summary of feedback from opening /Users/luca/Dropbox (Cambridge
University)/SARS_CoV_2_NSP1/PDB_DEPO/pdb:cif/27.05.2021.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 8
LEU A 20 1 13  
Start residue of secondary structure not found: HELIX 2 2 PRO A 22 VAL A 35 1
14  
Start residue of secondary structure not found: HELIX 3 3 LYS A 50 ASP A 52 1
3  
Start residue of secondary structure not found: HELIX 4 4 ASN A 62 LYS A 72 1
11  
Start residue of secondary structure not found: HELIX 5 5 ARG A 87 HIS A 91 1
5  
21 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 27 27 PRO B 285 ASN B 298
1 14  
Start residue of secondary structure not found: HELIX 28 28 ARG B 302 ILE B
316 1 15  
Start residue of secondary structure not found: HELIX 29 29 THR B 319 ILE B
332 1 14  
Start residue of secondary structure not found: HELIX 30 30 ASP B 337 GLY B
354 1 18  
Start residue of secondary structure not found: HELIX 31 31 SER B 366 SER B
373 1 8  
Start residue of secondary structure not found: HELIX 32 32 CYS B 384 TYR B
401 1 18  
1 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 34 34 HIS B 419 ASN B 433
1 15  
Start residue of secondary structure not found: HELIX 35 35 HIS B 443 ILE B
454 1 12  
Start residue of secondary structure not found: HELIX 36 36 GLU C 368 GLU C
371 1 4  
Start residue of secondary structure not found: HELIX 37 37 SER C 409 LYS C
426 1 18  
Start residue of secondary structure not found: HELIX 38 38 SER C 482 ARG C
491 1 10  
Start residue of secondary structure not found: HELIX 39 39 LYS C 522 VAL C
526 1 5  
31 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 71 71 LYS D 212 TYR D 235
1 24  
Start residue of secondary structure not found: HELIX 72 72 ASP D 275 SER D
280 1 6  
Start residue of secondary structure not found: HELIX 73 73 GLU D 332 ASP D
336 1 5  
Start residue of secondary structure not found: HELIX 74 74 TYR D 357 ARG D
371 1 15  
Start residue of secondary structure not found: HELIX 75 75 HIS D 386 ASN D
391 1 6  
Start residue of secondary structure not found: HELIX 76 76 PRO D 397 GLY D
412 1 16  
56 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 53 5353 ILE D 271 GLY D
274 0  
Start residue of secondary structure not found: SHEET 54 5454 GLN D 283 ASP D
287 0  
Start residue of secondary structure not found: SHEET 55 5555 SER D 295 LEU D
296 0  
Start residue of secondary structure not found: SHEET 56 5656 VAL D 301 ILE D
307 0  
Start residue of secondary structure not found: SHEET 57 5757 LEU D 314 LEU D
319 0  
Start residue of secondary structure not found: SHEET 58 5858 SER D 340 CYS D
346 0  
1 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 60 6060 HIS D 419 VAL D
423 0  
Start residue of secondary structure not found: SHEET 61 6161 VAL D 453 PHE D
455 0  
Start residue of secondary structure not found: SHEET 62 6262 CYS D 460 ILE D
464 0  
Start residue of secondary structure not found: SHEET 63 6363 ILE D 468 LEU D
471 0  
Start residue of secondary structure not found: SHEET 64 6464 ILE D 485 SER D
486 0  
Start residue of secondary structure not found: SHEET 65 6565 VAL D 537 ILE D
539 0  
6 messages similar to the above omitted  
  
Chain information for 27.05.2021.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select #2

19743 atoms, 20171 bonds, 46 pseudobonds, 2446 residues, 3 models selected  

> view sel

> hide #1 models

> show sel cartoons

> hide sel atoms

> select clear

> ui tool show "Side View"

> open 4vfm

Fetching url http://files.rcsb.org/download/4vfm.cif failed: HTTP Error 404:
Not Found  

> open 4fvm

Summary of feedback from opening 4fvm fetched from pdb  
---  
note | Fetching compressed mmCIF 4fvm from
http://files.rcsb.org/download/4fvm.cif  
  
4fvm title:  
Crystal structure of yeast DNA polymerase α [more info...]  
  
Chain information for 4fvm #3  
---  
Chain | Description  
A | DNA polymerase α catalytic subunit A  
  

> ui tool show Matchmaker

> matchmaker #3/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 27.05.2021.pdb, chain A (#2) with 4fvm, chain A (#3), sequence
alignment score = 1913.8  
RMSD between 516 pruned atom pairs is 1.113 angstroms; (across all 790 pairs:
4.703)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select clear

> select #2/A:409

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 6 atom styles  

> color sel byhetero

> select #2/A:405

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

137 atoms, 137 bonds, 18 residues, 1 model selected  

> show sel target ab

> style sel stick

Changed 137 atom styles  

> color sel byhetero

> select clear

> hide #!2 models

> select #3/A:887

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

412 atoms, 415 bonds, 27 residues, 1 model selected  

> view sel

> show sel atoms

> color sel byhetero

> select H

6732 atoms, 829 residues, 1 model selected  

> hide sel atoms

> select clear

> select #3/A:886

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

412 atoms, 415 bonds, 27 residues, 1 model selected  

> view sel

> select clear

> open 4fyd

Summary of feedback from opening 4fyd fetched from pdb  
---  
warnings | Atom HO5' is not in the residue template for C /E:1  
Atom HO5' is not in the residue template for C /F:1  
  
4fyd title:  
Crystal structure of yeast DNA polymerase α bound to DNA/RNA and dGTP [more
info...]  
  
Chain information for 4fyd #4  
---  
Chain | Description  
A B | DNA polymerase α catalytic subunit A  
C D | DNA
(5'-D(*TP*GP*ap*GP*CP*GP*TP*G*TP*GP*TP*ap*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')  
E F | DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*ap*G)-D(P*GP*G)-3')  
  
Non-standard residues in 4fyd #4  
---  
DGT — 2'-deoxyguanosine-5'-triphosphate  
  
4fyd mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> hide #!3 models

> select #4

29108 atoms, 29492 bonds, 72 pseudobonds, 1754 residues, 3 models selected  

> view sel

> show sel cartoons

> hide sel atoms

> select clear

> select #4/B:891

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

> select sel :< 10

1030 atoms, 1038 bonds, 9 pseudobonds, 76 residues, 3 models selected  

> show (#!4 & sel) target ab

> style sel & #!4 stick

Changed 694 atom styles  

> color sel & #!4 byhetero

> select H

21096 atoms, 2581 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select #4/B:889

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

> select clear

> select #4/B:891@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> view sel

> select clear

> ui tool show "Blast Protein"

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1632489728942-2089285466  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1632489728942-2089285466  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/A  
Failed HTTP Error 404:  
  

Could not fetch entry information for A  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 92, in on_finish  
self.tool.job_finished(self, p, self._params())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 284, in job_finished  
self._show_results(job.atomspec, blast_results)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 326, in _show_results  
self._add_pdbinfo(pdb_chains)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 345, in _add_pdbinfo  
data = info.fetch_info(self.session, chain_ids)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info  
entry, auth_cid = pcid.split('_')  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info  
entry, auth_cid = pcid.split('_')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.80.3.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H524)
      Kernel Version: Darwin 19.6.0
      Time since boot: 6 days 20:03

Graphics/Displays:

    Radeon Pro Vega 48:

      Chipset Model: Radeon Pro Vega 48
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6869
      Revision ID: 0x0000
      ROM Revision: 113-D0650E-072
      VBIOS Version: 113-D05001A1XG-011
      Option ROM Version: 113-D05001A1XG-011
      EFI Driver Version: 01.01.072
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    appdirs: 1.4.4
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    ChimeraX-AlignmentAlgorithms: 2.0
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    wheel: 0.34.2

[Eric Pettersen]

Hi Luca,

Thanks for reporting this problem. It is fixed in the 1.2.5 release, so if you get that you will be able to blast your sequence successfully.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab