Opened 6 years ago

Closed 6 years ago

#2682 closed defect (fixed)

Tape measure mouse mode error on map orthoplanes

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-12-12)
Description
Tape measure in orthoplanes mode gives this error.

Log:
UCSF ChimeraX version: 0.91 (2019-12-12)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\goddard\Desktop\vrdemos\opioids-vr-2018\ligands\beta-
> endorphin.pdb

Chain information for beta-endorphin.pdb #1  
---  
Chain | Description  
A | No description available  
  

> show atoms

> hide cartoons

> set bgColor white

> lighting soft

> style sphere

Changed 498 atom styles  

> rainbow

> show surfaces

> hide surfaces

> view orient

> graphics silhouettes true

> graphics silhouettes false

> open 20205 fromDatabase emdb

Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> volume step 2

> volume planes z orthoplanes off style solid

> ui mousemode rightMode "mark plane"

> marker #3 30.55,86.85,54.57 color yellow radius 1.07

> marker #3 68.65,72.88,54.57 color yellow radius 1.07

> ui mousemode rightMode "delete markers"

> marker delete #3:2

> volume style surface

> volume showOutlineBox true

> set bgColor black

> volume region all orthoplanes off

> volume #2 change image level -0.03835,0 level 0.3237,0.8 level 0.5169,1

> volume #2 level 0.2402

> ui mousemode rightMode "contour level"

> volume #2 level 0.1189

> volume #2 level 0.03763

> volume step 1

> style stick

Changed 499 atom styles  

> view

> view

> close #3

> view

> color byhetero

> lighting simple

> ui mousemode rightMode "bond rotation"

> torsion /A:31@HB2,CB,CA,N 112.59

> close

> open C:\Users\goddard\Desktop\vrdemos\dicom\Belarus_TB\20060710 format dicom

Opened CT 2, grid size 512,512,124, pixel 0.59,0.59,2.5, shown at step 1,
values int16  

> volume region all orthoplanes off

> volume appearance chest

> volume planes z orthoplanes off style solid

> mousemode right "move planes"

> volume #1.1.1.1 region 0,0,74,511,511,74

> mousemode right "crop volume"

> volume #1.1.1.1 region 0,0,74,511,511,91

> mousemode right "tape measure"

> marker segment #2 -112.6,76.37,-55.5 toPosition 90.91,73.65,-55.5 color
> yellow radius 0.1475 label 203.6 labelHeight 20.36 labelColor yellow

> mousemode right windowing

> volume #1.1.1.1 level -684.7,0 level -635.6,0.985 level -427.2,0 level
> 85.86,0.985 level 33.76,0 level 96.88,0.015 level -480.3,1 level 37.77,1
> level 321.3,0 level 343.4,1 level 3018,1

> volume #1.1.1.1 level -733.2,0 level -681.7,0.985 level -463.2,0 level
> 74.86,0.985 level 20.22,0 level 86.42,0.015 level -518.9,1 level 24.42,1
> level 321.8,0 level 344.9,1 level 3150,1

> view orient

> volume #1.1.1.1 level -733.2,0 level -681.7,0.985 level -463.2,0 level
> 74.86,0.985 level 20.22,0 level 86.42,0.015 level -518.9,1 level 24.42,1
> level 321.8,0 level 344.9,1 level 3150,1

> mousemode right "tape measure"

> marker delete #2

> volume appearance "Airways II"

> volume #1.1.1.1 orthoplanes xyz positionPlanes 256,256,62 style solid region
> all

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 469, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 398, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\atomic\tape_measure\tape.py", line 33, in mouse_down  
p, v = self._picked_point(event)  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\atomic\tape_measure\tape.py", line 140, in _picked_point  
pm, vm = method(xyz1, xyz2)  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\atomic\tape_measure\tape.py", line 178, in
_volume_maximum_point  
sxyz, v = first_volume_maxima(xyz1, xyz2, vlist)  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\markers\mouse.py", line 360, in first_volume_maxima  
v_xyz_in, v_xyz_out = data_slice(v, line)  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\markers\mouse.py", line 420, in data_slice  
xyz_in = xyz_out = slice.face_intercept_point(v, line)  
AttributeError: module 'chimerax.map.slice' has no attribute
'face_intercept_point'  
  
AttributeError: module 'chimerax.map.slice' has no attribute
'face_intercept_point'  
  
File "C:\Program Files\ChimeraX-Dec-12-2019\bin\lib\site-
packages\chimerax\markers\mouse.py", line 420, in data_slice  
xyz_in = xyz_out = slice.face_intercept_point(v, line)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.39
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Tom Goddard, 6 years ago

Component: UnassignedVolume Data
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionTape measure mouse mode error on map orthoplanes

comment:2 by Tom Goddard, 6 years ago

Resolution: fixed
Status: assignedclosed

Fixed

Tape measure did not consider orthoplanes (or boxfaces) as placing marker on a plane.

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