Blast Protein has trouble with sequences that include UNK

[Eric Pettersen]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005242323 (2020-05-24 23:23:37 UTC)
Description
Blast Protein has trouble with sequences that include UNK (e.g. 6bqn chain A) as per the log below.

Log:
UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6dg7 format mmcif fromDatabase pdb

6dg7 title:  
Full-length 5-HT3A receptor in a serotonin-bound conformation- State 1 [more
info...]  
  
Chain information for 6dg7 #1  
---  
Chain | Description  
A B C D E | 5-hydroxytryptamine receptor 3A  
  
Non-standard residues in 6dg7 #1  
---  
BMA — β-D-mannose  
NAG — N-acetyl-D-glucosamine  
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)  
  

> ui tool show "Blast Protein"

> blastprotein /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: appBlastProtein2Service1590532332282594450374  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1590532332282594450374  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> close

> open 6bqn format mmcif fromDatabase pdb

6bqn title:  
Cryo-EM structure of ENaC [more info...]  
  
Chain information for 6bqn #1  
---  
Chain | Description  
A | SCNN1A  
B | SCNN1B  
C | EGFP-SCNN1G chimera  
D | 7B1 fab  
E | 7B1 fab  
F | 10D4 fab  
G | 10D4 fab  
  

> sequence chain #1/A

Alignment identifier is 1.A  

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp2

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: appBlastProtein2Service1590532397706-446969987  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1590532397706-446969987  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
BlastProtein failed: BLAST query error: CFastaReader: Near line 2, there's a
line that doesn't look like plausible data, but it's not marked as defline or
comment.  
no element found: line 1, column 0  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      Boot ROM Version: 232.0.0.0.0
      SMC Version (system): 2.32f20

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 7:48

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Conrad Huang]

Fixed in 2ddcddb1e.

Use 'X' instead of '?' for unknown amino acids in BLAST FASTA input.