Opening BLAST hit: 'NoneType' object is not subscriptable

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Clicking on the link for a result in the Blast Protein tool.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open medioSMP.pdb

Summary of feedback from opening medioSMP.pdb  
---  
warning | Ignored bad PDB record found on line 2855  
END  
  
Chain information for medioSMP.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> "/run/media/tic20/storage/structure_dump/phasing_at_home/PARTICIPANT_3_ARMANDO_ALBERT/ORIGINAL
> DATA/data/SMP.seq"

Unrecognized file suffix '.seq'  

> open
> "/run/media/tic20/storage/structure_dump/phasing_at_home/PARTICIPANT_3_ARMANDO_ALBERT/ORIGINAL
> DATA/data/SMP.fasta"

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/__init__.py", line 63, in open  
format_name=name.upper(), **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
ValueError: No sequences found in FASTA file 'SMP.fasta'!  
  
ValueError: No sequences found in FASTA file 'SMP.fasta'!  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
  
See log for complete Python traceback.  
  

> open
> "/run/media/tic20/storage/structure_dump/phasing_at_home/PARTICIPANT_3_ARMANDO_ALBERT/ORIGINAL
> DATA/data/SMP.fasta"

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/phasing_at_home/PARTICIPANT_3_ARMANDO_ALBERT/ORIGINAL
DATA/data/SMP.fasta  
---  
note | Alignment identifier is SMP.fasta  
  
Opened 1 sequences from SMP.fasta  

> 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: appBlastProtein2Service1593868528261374335061  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1593868528261374335061  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Alignment identifier is bp1 [1]  
Associated medioSMP.pdb chain A to 4P42_A with 0 mismatches  

> open pdb:4P42

Summary of feedback from opening 4P42 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4p42 from
http://files.rcsb.org/download/4p42.cif  
Fetching CCD EGC from http://ligand-expo.rcsb.org/reports/E/EGC/EGC.cif  
  
4p42 title:  
Extended-Synaptotagmin 2, SMP - C2A - C2B Domains [more info...]  
  
Chain information for 4p42 #2  
---  
Chain | Description  
A B | Extended synaptotagmin-2  
  
Non-standard residues in 4p42 #2  
---  
EGC — 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-tetramethyl-
butyl)-phenoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol
(triton X-100)  
PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)  
  
Associated 4p42 chain A to 4P42_A with 0 mismatches  
Associated 4p42 chain B to 4P42_A with 0 mismatches  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
604, in customEvent  
func(*args, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 110, in handle_scheme  
self.load_pdb(url)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 369, in load_pdb  
models = run(self.session, "open pdb:%s" % pdb_id)[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 369, in load_pdb  
models = run(self.session, "open pdb:%s" % pdb_id)[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.36.06
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        5.6G         48G        221M        8.1G         56G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

This has been fixed in the daily build for a week or two. Hopefully we get 1.1 out the door sooner rather than later...