id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2276	Color zone on molecular surface error	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-24)
Description
Color zone on molecular surface gives this error.

Log:
UCSF ChimeraX version: 0.91 (2019-07-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1dg2 format mmCIF fromDatabase pdb

Summary of feedback from opening 1dg2 fetched from pdb  
---  
warning | Atom H1 is not in the residue template for GLY #1 in chain A  
  
1dg2 title:  
Solution conformation of A-conotoxin auib [more info...]  
  
Chain information for 1dg2  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | A-conotoxin auib  
  
  

> close #1.2-100

> surface

> color zone #1.1.1 near #1 distance 8 sharpEdges true

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command ""graphics restart"" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py"", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py"", line 164, in draw  
self._draw_scene(camera, drawings)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py"", line 230, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1418, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1429, in _draw_multiple  
d.draw(renderer, draw_pass)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 715, in draw  
self.draw_self(renderer, draw_pass)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 722, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 746, in _draw_geometry  
self._update_buffers()  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 864, in _update_buffers  
dss.update_element_buffer(ta, style, tmsel, em)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1633, in
update_element_buffer  
self.elements = e = self.masked_elements(triangles, style, triangle_mask,
edge_mask)  
File ""/Users/goddard/Desktop/ChimeraX July 24
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py"", line 1652, in masked_elements  
ta = ta[tmask, :]  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 28524 but corresponding boolean dimension is 23424  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	normal		Surface		fixed						all	ChimeraX