Opened 5 years ago

Closed 5 years ago

#3454 closed defect (fixed)

Volume backing color wrong position if volume moved

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:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202006250254 (2020-06-25 02:54:05 UTC)
Description
Volume image display backing color appears in the wrong place if the volume has been translated with move model mouse mode.  Looks like it ignores the move.

Log:
UCSF ChimeraX version: 1.1.dev202006250254 (2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/cov2_rna_twist.cxs format session

Log from Sat Jun 6 17:27:41 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/Desktop/cov2_rna_twist.cxs format session

Log from Sat Jun 6 17:17:30 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere length
> 500 randomLoopTwist 180

RNA sphere radius 47.8  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> style stick

Changed 11096 atom styles  

> hide #1 models

> close

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere
> randomLoopTwist 180

RNA sphere radius 340.4  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> hide #1 models

> lighting soft

> lighting simple

> lighting soft

> set bgColor white

> set bgColor black

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> shape sphere color black

> hide #2 models

> set bgColor white

> close #3

> show #2 models

> shape sphere color black radius 400

> close #3

> shape sphere color black radius 350

> close #3

> shape sphere color black radius 300

> close #3

> shape sphere color black radius 340

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting full

> lighting soft

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> close #1

> rename #2 id #4

> rename #3 id #4.1

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/rdv.pdb

> hide #4 models

> rename #2 id #1

> set bgColor black

> show #4 models

> hide #4 models

> lighting simple

> show #4 models

> hide #4 models

> view

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/atp.pdb

> ui mousemode right "translate selected models"

> select #2:1@O6

1 atom, 1 model selected  

> select clear

> color #1 & C tan

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/rtp.pdb

> select #3:1@O12

1 atom, 1 model selected  

> select clear

> rename #1 Remdesivir

> rename #2 ATP

> rename #3 RTP

> rename #4 "SARS-CoV-2 RNA"

> rename #4.1 sphere

> show #4 models

> select #1-3

165 atoms, 172 bonds, 3 models selected  

> hide #4 models

> show #4 models

> select clear

> save data/remdesivir1.cxs

> select #1-3

165 atoms, 172 bonds, 3 models selected  

> select clear

> open 7bv2

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #5  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #5  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> hide #4 models

> select #5/A:133@ND1

1 atom, 1 model selected  

> show #4 models

> lighting simple

> set bgColor white

> select clear

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir1.cxs

> hide #2 models

> hide #3 models

> set bgColor black

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/7bv2_particles.tif

Opened 7bv2_particles.tif, grid size 1600,1654,1, pixel 1, shown at step 1,
values uint8  

> hide #1 models

> hide #4 models

> hide #!5 models

> volume #6 level 105,0 level 223,0.8 level 255,1

> volume #6 level 105,0 level 179.6,0.9853 level 255,1

> volume #6 level 18.43,0.9853 level 179.6,0.9853 level 255,1

> volume #6 level 18.43,0.9853 level 179.6,0.9853 level 249.5,0

> volume #6 level 18.43,0.9853 level 144.7,0.4118 level 249.5,0

> volume #6 level 18.43,0.9853 level 144.7,0.4118 level 255,1

> volume #6 level 18,0.02941 level 144.7,0.4118 level 255,1

> volume #6 level 18,0.02941 level 255,1 color white color white

> volume #6 level 18,0 level 255,1

> show #!5 models

> ui mousemode right "tape measure"

> marker segment #7 position 1438,1513,0 toPosition 1560,1524,1.137e-13 color
> yellow radius 0.25 label 122.7 labelHeight 12.27 labelColor yellow

> marker delete #7

> marker segment #7 position 1434,1615,0 toPosition 1562,1612,-1.137e-13 color
> yellow radius 0.25 label 128.2 labelHeight 12.82 labelColor yellow

> volume #6 voxelSize 2.34

> select clear

> marker segment #7 position 3357,3776,0 toPosition 3654,3774,0 color yellow
> radius 0.585 label 296.7 labelHeight 29.67 labelColor yellow

> select clear

> marker delete #7

> ui mousemode right "translate selected models"

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir1.cxs

> select #6

2 models selected  

> show #4 models

> hide #4 models

> set bgColor white

> set bgColor black

> volume #6 level 18,0 level 255,1 level 135.9,0.6471 color white color white
> color white

> volume #6 level 18,0 level 255,1 level 137.6,0.6912

> volume #6 level 101.8,0 level 255,1 level 137.6,0.6912

> volume #6 level 101.8,0 level 255,1 level 137.1,0.6324

> volume #6 level 19.28,0 level 255,1 level 137.1,0.6324

> volume #6 level 19.28,0 level 255,1 level 201,1

> volume #6 level 18,1 level 255,1 level 201,1

> volume #6 level 18,1 level 255,0 level 201,1

> volume #6 level 18,1 level 255,0 level 117.1,0.7059

> volume #6 level 18,0 level 255,0 level 117.1,0.7059

> volume #6 level 18,0 level 255,1 level 117.1,0.7059

> volume #6 level 18,0 level 255,1 level 183.9,0.6618

> volume #6 level 18,0 level 255,1 level 179.3,0.6912

> volume #6 level 18,0 level 255,1 color white color white

> set bgColor white

> volume #6 backingColor black

> ui tool show Shell




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 21:01

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Tom Goddard, 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 backing color wrong position if volume moved

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Backing color was always being positioned as if position was identity matrix.

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