Opened 5 years ago

Closed 5 years ago

#3316 closed task (not a bug)

Test if bug report log contains all commands

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

Description 

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005210540 (2020-05-21 05:40:33 UTC)
Description
Checking to see if log contains all commands in bug report.

Log:
Startup Messages  
---  
warnings | QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already
registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
8 messages similar to the above omitted  
Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
Replacing opener for 'Gromacs full-precision coordinates' from MD-crds bundle
with that from MDcrds bundle  
Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle with
that from MDcrds bundle  
Replacing opener for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
notes | Replacing data format 'Gromacs full-precision coordinates' as defined
by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-
MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds bundle
with definition from ChimeraX-MDcrds bundle  
  
UCSF ChimeraX version: 1.0rc202005220158 (2020-05-21)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6cgv

Summary of feedback from opening 6cgv fetched from pdb  
---  
note | Fetching compressed mmCIF 6cgv from
http://files.rcsb.org/download/6cgv.cif  
  
6cgv title:  
Revised crystal structure of human adenovirus [more info...]  
  
Chain information for 6cgv #1  
---  
Chain | Description  
A B C D E F G H I J K L | Hexon protein  
M | Pre-hexon-linking protein IIIa  
N | Penton protein  
P Q R S | Hexon-interlacing protein  
U V | Pre-hexon-linking protein VIII  
W | Pre-protein VI  
  
6cgv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> split #1

Chain information for 6cgv A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6cgv B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6cgv C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6cgv D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 6cgv E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 6cgv F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 6cgv G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 6cgv H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 6cgv I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 6cgv J #1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 6cgv K #1.11  
---  
Chain | Description  
K | No description available  
  
Chain information for 6cgv L #1.12  
---  
Chain | Description  
L | No description available  
  
Chain information for 6cgv M #1.13  
---  
Chain | Description  
M | No description available  
  
Chain information for 6cgv N #1.14  
---  
Chain | Description  
N | No description available  
  
Chain information for 6cgv P #1.15  
---  
Chain | Description  
P | No description available  
  
Chain information for 6cgv Q #1.16  
---  
Chain | Description  
Q | No description available  
  
Chain information for 6cgv R #1.17  
---  
Chain | Description  
R | No description available  
  
Chain information for 6cgv S #1.18  
---  
Chain | Description  
S | No description available  
  
Chain information for 6cgv U #1.19  
---  
Chain | Description  
U | No description available  
  
Chain information for 6cgv V #1.20  
---  
Chain | Description  
V | No description available  
  
Chain information for 6cgv W #1.21  
---  
Chain | Description  
W | No description available  
  
Split 6cgv (#1) into 21 models  

> close #1.4-21

> sym #1 I,222r

> shape icosahedron radius 450 orientation 222r mesh true divisions 2

> ui tool show "Side View"

> usage distance style

distance style [pbonds] [color a color] [dashes dashes] [radius a number]
[decimalPlaces decimalPlaces] [symbol true or false] [setDefaults true or
false]  
— set distance display properties  
pbonds: a pseudobonds specifier or nothing  
dashes: an integer ≥ 0  
decimalPlaces: an integer ≥ 0  

> ui mousemode right distance

> select #1.1/A:72@OD1

1 atom, 1 model selected  

> select clear

> hide #2 models

> distance #1.1/A:73@NE #1.3/C:54@CA

Distance between 6cgv A #1.1/A ARG 73 NE and 6cgv C #1.3/C HIS 54 CA: 61.810Å  

> show #2 models

> distance style radius 0.1

> distance #1.2/B:255@OD1 #1.2/B:255@ND2

Distance between 6cgv B #1.2/B ASN 255 OD1 and ND2: 2.252Å  

> show cartoons

> view name facet

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

> close

> open 6cgv

6cgv title:  
Revised crystal structure of human adenovirus [more info...]  
  
Chain information for 6cgv #1  
---  
Chain | Description  
A B C D E F G H I J K L | Hexon protein  
M | Pre-hexon-linking protein IIIa  
N | Penton protein  
P Q R S | Hexon-interlacing protein  
U V | Pre-hexon-linking protein VIII  
W | Pre-protein VI  
  
6cgv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> split #1

Chain information for 6cgv A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6cgv B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6cgv C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6cgv D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 6cgv E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 6cgv F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 6cgv G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 6cgv H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 6cgv I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 6cgv J #1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 6cgv K #1.11  
---  
Chain | Description  
K | No description available  
  
Chain information for 6cgv L #1.12  
---  
Chain | Description  
L | No description available  
  
Chain information for 6cgv M #1.13  
---  
Chain | Description  
M | No description available  
  
Chain information for 6cgv N #1.14  
---  
Chain | Description  
N | No description available  
  
Chain information for 6cgv P #1.15  
---  
Chain | Description  
P | No description available  
  
Chain information for 6cgv Q #1.16  
---  
Chain | Description  
Q | No description available  
  
Chain information for 6cgv R #1.17  
---  
Chain | Description  
R | No description available  
  
Chain information for 6cgv S #1.18  
---  
Chain | Description  
S | No description available  
  
Chain information for 6cgv U #1.19  
---  
Chain | Description  
U | No description available  
  
Chain information for 6cgv V #1.20  
---  
Chain | Description  
V | No description available  
  
Chain information for 6cgv W #1.21  
---  
Chain | Description  
W | No description available  
  
Split 6cgv (#1) into 21 models  

> close #1.4-21

> sym #1 I,222r

> show surfaces

> shape icosahedron radius 450 orientation 222r mesh true divisions 2

> ui mousemode right distance

> distance #1.2/B:278@CG #1.2/B:192@OG1

Distance between 6cgv B #1.2/B ASP 278 CG and THR 192 OG1: 29.224Å  

> distance style radius 0.1

> view name facet

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

> select #1

22014 atoms, 22606 bonds, 4 pseudobonds, 8 models selected  

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

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

Alignment identifier is 1.1.A  

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




OpenGL version: 4.1 ATI-3.8.24
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: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 17 days 13:55

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 → Command Line
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Test if bug report log contains all commands
Type: defect → task

comment:2 by Tom Goddard, 5 years ago

Resolution: → not a bug
Status: assigned → closed

All commands in this test seemed to make it into the bug report log.

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