error using BLOSUM100 in blast

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-23)
Description
error when blast protein returned xml.etree.ElementTree.ParseError: no element found: line 1, column 0

Maybe due to using a Modeller output model as query chain.  I had a complicated session.  Will try to make a simpler session and test this theory.

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> open presets.cxc

> alias cardef car style modeh def arrows t arrowshelix f arrowscale 2 wid 2
thick 0.4 sides 12 div 20; car style ~(nucleic|strand) x round; car style
(nucleic|strand) x rect

> alias nospheres style (protein|nucleic|solvent) & @@draw_mode=0 stick

> alias nucrib cardef; car style nucleic x round width 1.6 thick 1.6

> alias cylinders cardef; car style protein modeh tube rad 2 sides 24 thick
0.6

> alias licorice cardef; car style protein modeh default arrows f x round
width 1 thick 1

> alias cartoon1 surf hide; nospheres; cartoon; cardef; nuc tube/slab shape
box

> alias cartoon2 surf hide; nospheres; cartoon; cylinders; car style nucleic x
round width 1.6 thick 1.6; nuc stubs

> alias cartoon3 surf hide; nospheres; cartoon; licorice; car style nucleic x
round width 1.6 thick 1.6; nuc tube/slab shape ellipsoid

> alias surfw nospheres; surface; color white targ s trans 80

> alias surfat nospheres; surface; color fromatoms targ s trans 70

> alias surfc nospheres; surface; color bychain targ s trans 0

> alias surfm nospheres; surface; color bymodel targ s trans 0

> alias pub set bgcolor white silhouettes t

> alias unpub ~set bgcolor; set silhouettes f

executed presets.cxc  
executed startup.cxc  
UCSF ChimeraX version: 0.9 (2019-04-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/meng/Desktop/junk.cxs

Summary of feedback from opening /Users/meng/Desktop/junk.cxs  
---  
notes | Associated target (2.1) chain B to 1ireb with 0 mismatches  
Associated target (2.2) chain B to 1ireb with 0 mismatches  
Associated target (2.3) chain B to 1ireb with 0 mismatches  
Associated 1ire chain B to 1ireb with 0 mismatches  
  
opened ChimeraX session  

> help help:user/tools/blastprotein.html

> help blast

> toolshed show Blast

> blastprotein #2.1/A database pdb cutoff 1e-3 matrix BLOSUM100 max_seqs 20
tool_id 29

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: appBlastProtein2Service1556052002760-43159332  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1556052002760-43159332  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 537, in customEvent  
func(*args, **kw)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 93, in on_finish  
p = Parser("query", self.seq, results)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/xml/etree/ElementTree.py",
line 1316, in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/xml/etree/ElementTree.py",
line 1316, in XML  
return parser.close()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.8.38
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Elaine Meng]

Nope it was not from using the Modeller result as input chain. I get the same error with any protein query and default Blast Protein settings except changing matrix to BLOSUM100. Seems to happen when the results are returned.

[Conrad Huang]

Fixed in 7510c8922.

The list of supported similarity matrices in BLAST changed, so BLOSUM100 was no longer valid. Code was changed to report BLAST error output when parsing fails, and the list of matrices was updated.