UniProt fetch: HTTP Error 405: Not Allowed

[marc.bjorklund@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
I wanted to access the uniprot database for my protein through the uniprot column in the chain information (after opening the database with the command: "open 6bqv"). This causes an error. 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6bqv

Summary of feedback from opening 6bqv fetched from pdb  
---  
notes | Fetching compressed mmCIF 6bqv from
http://files.rcsb.org/download/6bqv.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching CCD Y01 from http://ligand-expo.rcsb.org/reports/Y/Y01/Y01.cif  
  
6bqv title:  
Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state [more
info...]  
  
Chain information for 6bqv #1  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily M member 4 |
TRPM4_HUMAN  
  
Non-standard residues in 6bqv #1  
---  
CA — calcium ion  
Y01 — cholesterol hemisuccinate  
  

> log metadata #1

Metadata for 6bqv #1  
---  
Title | Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state  
Citation | Autzen, H.E., Myasnikov, A.G., Campbell, M.G., Asarnow, D., Julius,
D., Cheng, Y. (2018). Structure of the human TRPM4 ion channel in a lipid
nanodisc. Science, 359, 228-232. PMID: 29217581. DOI: 10.1126/science.aar4510  
Non-standard residues | CA — calcium ion  
Y01 — cholesterol hemisuccinate  
Gene source | Homo sapiens (human)  
Experimental method | Electron microscopy  
Resolution | 3.1Å  
  
> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

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

Alignment identifier is 1  

> hide target m

[Repeated 3 time(s)]

> close

> open 6bqv format mmcif fromDatabase pdb

6bqv title:  
Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state [more
info...]  
  
Chain information for 6bqv #1  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily M member 4 |
TRPM4_HUMAN  
  
Non-standard residues in 6bqv #1  
---  
CA — calcium ion  
Y01 — cholesterol hemisuccinate  
  

> open 6bqv

6bqv title:  
Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state [more
info...]  
  
Chain information for 6bqv #2  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily M member 4 |
TRPM4_HUMAN  
  
Non-standard residues in 6bqv #2  
---  
CA — calcium ion  
Y01 — cholesterol hemisuccinate  
  

> interfaces ~solvent

20 buried areas: #2/C #1/C 24354, #2/A #1/A 24354, #2/B #1/B 24353, #2/D #1/D
24353, #2/B #2/D 3814, #2/B #1/D 3814, #2/D #1/B 3814, #1/B #1/D 3814, #2/C
#1/A 3797, #1/A #1/C 3797, #2/A #2/C 3797, #2/A #1/C 3797, #2/C #2/D 3789,
#2/C #1/D 3789, #2/D #1/C 3789, #1/C #1/D 3789, #2/A #2/B 3787, #2/A #1/B
3787, #2/B #1/A 3787, #1/A #1/B 3787  

> ui windowfill toggle

[Repeated 1 time(s)]

> open 6bqv format mmcif fromDatabase pdb

6bqv title:  
Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state [more
info...]  
  
Chain information for 6bqv #3  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily M member 4 |
TRPM4_HUMAN  
  
Non-standard residues in 6bqv #3  
---  
CA — calcium ion  
Y01 — cholesterol hemisuccinate  
  
Alignment identifier is 1  

> interfaces ~solvent

48 buried areas: #2/C #1/C 24354, #2/C #3/C 24354, #1/C #3/C 24354, #2/A #1/A
24354, #2/A #3/A 24354, #1/A #3/A 24354, #2/B #1/B 24353, #2/B #3/B 24353,
#1/B #3/B 24353, #2/D #1/D 24353, #1/D #3/D 24353, #2/D #3/D 24353, #2/B #2/D
3814, #2/B #1/D 3814, #2/D #1/B 3814, #2/D #3/B 3814, #1/B #1/D 3814, #1/D
#3/B 3814, #2/B #3/D 3814, #1/B #3/D 3814, #3/B #3/D 3814, #2/C #1/A 3797,
#2/C #3/A 3797, #1/A #1/C 3797, #1/C #3/A 3797, #3/A #3/C 3797, #2/A #2/C
3797, #2/A #1/C 3797, #2/A #3/C 3797, #1/A #3/C 3797, #2/C #2/D 3789, #2/C
#1/D 3789, #2/C #3/D 3789, #2/D #1/C 3789, #1/C #1/D 3789, #1/C #3/D 3789,
#1/D #3/C 3789, #3/C #3/D 3789, #2/D #3/C 3789, #2/A #2/B 3787, #2/A #1/B
3787, #2/A #3/B 3787, #2/B #1/A 3787, #2/B #3/A 3787, #1/B #3/A 3787, #3/A
#3/B 3787, #1/A #1/B 3787, #1/A #3/B 3787  

> ~hbonds

[Repeated 2 time(s)]

> hbonds reveal true

23553 hydrogen bonds found  

> log metadata #1

Metadata for 6bqv #1  
---  
Title | Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state  
Citation | Autzen, H.E., Myasnikov, A.G., Campbell, M.G., Asarnow, D., Julius,
D., Cheng, Y. (2018). Structure of the human TRPM4 ion channel in a lipid
nanodisc. Science, 359, 228-232. PMID: 29217581. DOI: 10.1126/science.aar4510  
Non-standard residues | CA — calcium ion  
Y01 — cholesterol hemisuccinate  
Gene source | Homo sapiens (human)  
Experimental method | Electron microscopy  
Resolution | 3.1Å  
  
> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

> open TRPM4_HUMAN fromDatabase uniprot

Error from UniProt web server: HTTP Error 405: Not Allowed  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 16:04

Graphics/Displays:

    Apple G13G:

      Chipset Model: Apple G13G
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
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    ChimeraX-ColorKey: 1.5.1
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    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.1.2
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Marc,

Thanks for reporting this problem. UniProt changed the API for fetching sequence information from their website since the ChimeraX 1.4 release. If you get the current daily build, UniProt fetching will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab