id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1742	volume onesmask: local variable 'varray' referenced before assignment	a.rohou@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-22)
Description
Please see log for steps to reproduce

Log:
UCSF ChimeraX version: 0.9 (2019-02-22)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help open

> open emdb:0341

Summary of feedback from opening 0341 fetched from emdb  
---  
note | Fetching compressed map 0341 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0341/map/emd_0341.map.gz  
  
Opened emd_0341.map, grid size 360,360,360, pixel 1.2, shown at level 0.00384,
step 2, values float32  

> open pdb:6n4q

6n4q title:  
CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating
modifier toxin ProTx2 [more info...]  
  
Chain information for 6n4q #2  
---  
Chain | Description  
A B C D | Nav1.7 VSD2-NavAb chimera  
E F G H | Beta/omega-theraphotoxin-Tp2a  
I K | Fab light chain  
J L | Fab heavy chain  
  
  

> ribbon #2

> ~show #2

> molmap #2 20.0 onGrid #1

> help volume onesmask

> volume onesmask #3.1

Traceback (most recent call last):  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py"", line 253, in execute  
cmd.run(cmd_text)  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2617, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/maskcommand.py"", line 72, in ones_mask  
model_id = model_id)  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/maskcommand.py"", line 43, in mask  
fill_overlap, extend, model_id)  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py"", line 96, in masked_volume  
volume)  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py"", line 157, in
surface_projection_coordinates  
varray = tfrs.transform_points(varray)  
UnboundLocalError: local variable 'varray' referenced before assignment  
  
UnboundLocalError: local variable 'varray' referenced before assignment  
  
File
""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py"", line 157, in
surface_projection_coordinates  
varray = tfrs.transform_points(varray)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.36.23
OpenGL renderer: Intel(R) Iris(TM) Graphics 650
OpenGL vendor: Intel Inc.

}}}
"	defect	closed	normal		Volume Data		fixed						all	ChimeraX