Opened 2 years ago

Closed 2 years ago

#9976 closed defect (fixed)

Fetching PDB biounit shows error in status line

Reported by: meng@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202309121847 (2023-09-12 18:47:21 UTC)
Description
Fetching pdbe_bio 6ts0 says in the secondary status line (right side): "Error fetching 6ts0 bioassembly 2".

I believe this is because there is only 1 bioassembly but the code does not know how many there are and just tries to keep reading additional ones until it gets an error.  Elaine reported this.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.7.dev202309121847 (2023-09-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6ts0 fromDatabase pdbe_bio ignoreCache true

Summary of feedback from opening 6ts0 fetched from pdbe_bio  
---  
warnings | Atom H is not in the residue template for SER /A:6  
Atom H is not in the residue template for SER /AA:6  
Atom H is not in the residue template for SER /AB:6  
Atom H is not in the residue template for SER /AC:6  
Atom H is not in the residue template for SER /AD:6  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Fetching compressed 6ts0 bioassembly 1 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6ts0-assembly-1.cif.gz  
Combining 4 symmetry atoms into HOH /MA:415 O  
Combining 4 symmetry atoms into FE /FA:205 FE  
Combining 4 symmetry atoms into HOH /MA:318 O  
Combining 3 symmetry atoms into FE /HM:207 FE  
Combining 3 symmetry atoms into FE /HA:207 FE  
Combining 3 symmetry atoms into FE /HB:207 FE  
Combining 3 symmetry atoms into FE /HO:207 FE  
Combining 3 symmetry atoms into FE /EM:204 FE  
11 messages similar to the above omitted  
Combining 4 symmetry atoms into HOH /ME:415 O  
Combining 4 symmetry atoms into FE /FE:205 FE  
Combining 4 symmetry atoms into HOH /ME:318 O  
Combining 4 symmetry atoms into HOH /MI:415 O  
Combining 4 symmetry atoms into FE /FI:205 FE  
7 messages similar to the above omitted  
Combining 3 symmetry atoms into HOH /MC:449 O  
Combining 3 symmetry atoms into HOH /MN:449 O  
Combining 3 symmetry atoms into HOH /ML:449 O  
Combining 3 symmetry atoms into HOH /M:449 O  
Combining 3 symmetry atoms into FE /JC:209 FE  
11 messages similar to the above omitted  
Combining 4 symmetry atoms into HOH /M:318 O  
Combining 4 symmetry atoms into FE /F:205 FE  
Combining 4 symmetry atoms into HOH /M:415 O  
  
6ts0 bioassembly 1 title:  
Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A
Fe(III)-loaded for 30 minutes [more info...]  
  
Chain information for 6ts0 bioassembly 1 #1  
---  
Chain | Description  
A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW |
Ferritin light chain  
  
Non-standard residues in 6ts0 bioassembly 1 #1  
---  
CD — (CD)  
FE — (FE)  
O — (O)  
  
6ts0 bioassembly 1 mmCIF Assemblies  
---  
1| author_defined_assembly  
  
Opened 1 biological assemblies for 6ts0  

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OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 515.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 34 days, 23 hours, 47 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
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    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-BondRot: 2.0.4
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    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
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    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
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    ChimeraX-Tug: 1.0.1
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    ChimeraX-VIPERdb: 1.0
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    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
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Change History (2)

comment:1 by Tom Goddard, 2 years ago

Component: UnassignedInput/Output
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Reporter: changed from goddard@… to meng@…
Status: newassigned
Summary: ChimeraX bug report submissionFetching PDB biounit shows error in status line

comment:2 by Tom Goddard, 2 years ago

Resolution: fixed
Status: assignedclosed

Fixed.

As suspected, ChimeraX does not know how many bioassemblies there are and just keeps fetching files with higher suffix numbers until an error occurs. Made that error not appear in the status line.

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