id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1885	error using BLOSUM100 in blast	Elaine Meng	Conrad Huang	"{{{
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.

}}}
"	defect	closed	normal		Sequence		fixed						all	ChimeraX