Opened 5 years ago

Closed 5 years ago

#3989 closed defect (fixed)

"volume boxes" attempts to a model to scene twice

Reported by: caillancm@… 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:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
I selected a single atom visually, then used 'volume boxes' to exract part of a map. The operation worked as expected: one more map reboxed around the selected atom was created. The only indication anything went wrong was this error message.

When trying a similar operation but with a residue selected, one new volume for each atom in the selection was created.

Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> set bgColor white

> open /Users/crowe/Dropbox/poxtA/maps/r3d/j150_1cl3d_large_run_class001.mrc

Opened j150_1cl3d_large_run_class001.mrc as #1, grid size 420,420,420, pixel
0.82, shown at level 0.0153, step 2, values float32  

> volume #1 level 0.01328

> volume #1 level 0.007411

> open /Users/crowe/Dropbox/poxtA/masks/j150_1cl3d_solvent_mask.mrc

Opened j150_1cl3d_solvent_mask.mrc as #2, grid size 420,420,420, pixel 0.82,
shown at level 1, step 2, values float32  

> volume #2 level 1

> volume #1 level 0.002652

> volume #1 level 0.00245

> volume #1 level 0.0026

> close #2

> open /Users/crowe/Dropbox/poxtA/masks/mask.mrc

Opened mask.mrc as #2, grid size 420,420,420, pixel 0.82, shown at level 1,
step 2, values float32  

> volume #2 level 1

> close #2

> open /Users/crowe/Dropbox/poxtA/masks/mask.mrc

Opened mask.mrc as #2, grid size 420,420,420, pixel 0.82, shown at level 1,
step 2, values float32  

> volume #2 level 1

> close #2

> open /Users/crowe/Dropbox/poxtA/masks/mask.mrc

Opened mask.mrc as #2, grid size 420,420,420, pixel 0.82, shown at level 1,
step 2, values float32  

> volume #2 level 1

> volume #1 level 0.002398

> close #2

> open /Users/crowe/Dropbox/poxtA/masks/mask.mrc

Opened mask.mrc as #2, grid size 420,420,420, pixel 0.82, shown at level 1,
step 2, values float32  

> volume #2 level 1

> open /Users/crowe/Dropbox/poxtA/masks/As-fc_cl1_no-A_ref_j049_mask.mrc

Opened As-fc_cl1_no-A_ref_j049_mask.mrc as #3, grid size 420,420,420, pixel
0.82, shown at level 1, step 2, values float32  

> volume #3 level 1

> close #3

> volume #2 level 1

> close #2

> open /Users/crowe/Dropbox/poxtA/masks/mask.mrc

Opened mask.mrc as #2, grid size 420,420,420, pixel 0.82, shown at level 1,
step 2, values float32  

> volume #2 level 1

> volume #2 level 1

> close session

> open /Users/crowe/Dropbox/ABCF-
> writing/models/lsaA-70S/201127_lsaA-70S_RSR07_06-coot-0.pdb

Chain information for 201127_lsaA-70S_RSR07_06-coot-0.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/crowe/Dropbox/ABCF-writing/maps/pp/pp_LsaA_cl2-4_rebox-
> resamp.mrc

Opened pp_LsaA_cl2-4_rebox-resamp.mrc as #2, grid size 352,352,352, pixel
1.04, shown at level 0.0217, step 2, values float32  

> hide atoms

> show cartoons

> select /0:455

8 atoms, 7 bonds, 1 residue, 1 model selected  

> volume boxes #2 centers sel size 50

Opened box /0 ASN 455 N as #3, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CA as #4, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 C as #5, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 O as #6, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CB as #7, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CG as #8, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 OD1 as #9, grid size 50,50,50, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 ND2 as #10, grid size 50,50,50, pixel 1.04, shown at
step 1, values float32  

> volume boxes #2 centers sel size 20

Opened box /0 ASN 455 N as #12, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CA as #13, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 C as #14, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 O as #15, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CB as #16, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 CG as #17, grid size 22,22,22, pixel 1.04, shown at step
1, values float32  
Opened box /0 ASN 455 OD1 as #18, grid size 22,22,22, pixel 1.04, shown at
step 1, values float32  
Opened box /0 ASN 455 ND2 as #19, grid size 21,21,21, pixel 1.04, shown at
step 1, values float32  

> close #11,20#2-10,12-19

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select clear

> select /0:455@ND2

1 atom, 1 residue, 1 model selected  

> volume boxes #2 centers sel size 20

> hide #!1 models

> show #!1 models

> open /Users/crowe/Dropbox/ABCF-writing/maps/pp/pp_LsaA_cl2-4_rebox-
> resamp.mrc

Opened pp_LsaA_cl2-4_rebox-resamp.mrc as #2, grid size 352,352,352, pixel
1.04, shown at level 0.0217, step 2, values float32  

> volume boxes #2 centers sel size 20

Opened box /0 ASN 455 ND2 as #3, grid size 21,21,21, pixel 1.04, shown at step
1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/vopcommand.py", line 503, in volume_boxes  
bv = boxes(session, v, centers, size, isize, use_marker_size, step, subregion,
model_id)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/boxes.py", line 52, in boxes  
session.models.add(vlist)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 643, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model box /0 ASN 455 ND2 #3 to scene twice  
  
ValueError: Attempted to add model box /0 ASN 455 ND2 #3 to scene twice  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 643, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  

> close #3

> volume boxes #2 centers sel size 40

Opened box /0 ASN 455 ND2 as #3, grid size 41,41,41, pixel 1.04, shown at step
1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/vopcommand.py", line 503, in volume_boxes  
bv = boxes(session, v, centers, size, isize, use_marker_size, step, subregion,
model_id)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/boxes.py", line 52, in boxes  
session.models.add(vlist)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 643, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model box /0 ASN 455 ND2 #3 to scene twice  
  
ValueError: Attempted to add model box /0 ASN 455 ND2 #3 to scene twice  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 643, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      Boot ROM Version: 1037.140.50.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 9 days 22:28

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
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          Online: Yes
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        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: YPPY075J05DS
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
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Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "volume boxes" attempts to a model to scene twice

Reported by Caillan Crowe-McAuliffe

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's ChimeraX daily builds.

Volume boxes command was opening the new box models twice as the error message said. Trouble was volume_from_grid_data() by default opens the newly created volume, then the code explicitly opened the box model after that.

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