Non-functional selectors

[phil.cruz@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
When I open the attached file, and then define a series of user-defined selectors,  choosing these named selections gives the message "Nothing Selected". Somehow the definitions are lost, and indeed nothing is selected.

Here are the commands:
select  :1-49,135-196,282-295
name domain1 sel
color sel red
sel :50-99, 109-134,193-281
name domain2 sel
color sel yellow
sel :297-395
name domain3 sel
color sel blue
sel :100-109
name fusion sel
color sel green
sel :396-453
name stem sel
color sel hot pink
sel :454-495
name membrane sel
color sel pink 

Log:
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/Schrodinger/fluoroquinolones/model1/InducedFit_model1/InducedFit_model1_rec.mae"
> format "schrodinger maestro" maestro

Expected a keyword  

> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/Schrodinger/fluoroquinolones/model1/InducedFit_model1/InducedFit_model1_rec.mae"

Chain information for InducedFit_model1_rec.mae #1  
---  
Chain | Description  
| No description available  
  
Opened InducedFit_model1_rec.mae containing 1 structures (7563 atoms, 7644
bonds)  

> select :1-49,135-196,282-295

1904 atoms, 1919 bonds, 1 model selected  

> name domain1 sel

> color sel red

> select :50-99, 109-134,193-281

2567 atoms, 2592 bonds, 1 model selected  

> name domain2 sel

> color sel yellow

> select :297-395

1522 atoms, 1538 bonds, 1 model selected  

> name domain3 sel

> color sel blue

> select :100-109

123 atoms, 125 bonds, 1 model selected  

> name fusion sel

> color sel green

> select :396-453

862 atoms, 872 bonds, 1 model selected  

> name stem sel

> color sel hot pink

> select :454-495

651 atoms, 656 bonds, 1 model selected  

> name membrane sel

> color sel pink

> select clear

> select domain1

Nothing selected  




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 204.0.0.0.0
      SMC Version (system): 2.45f0

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 12 days 16:16

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      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
          Rotation: Supported
          Automatically Adjust Brightness: No
        BenQ GW2750H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6CD03450SL0 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C Digital AV Adapter
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 2.35
File attachment: InducedFit_model1_rec.mae

InducedFit_model1_rec.mae​

[phil.cruz@…]

Added by email2trac

[Eric Pettersen]

Hi Phil,

The basic "name" command takes literally what you typed as an argument and remembers it, then reapplies it each time you use it. So if you give "sel" as the argument then every time you use the selector you will get the current contents of the selection. Conversely, the "name frozen" command takes its argument and finds out what it currently expands to and remembers that instead. So you had two options here, either a series of commands like:

select :1-49,135-196,282-295
name frozen domain1 sel
color sel red

or like:

name domain1 :1-49,135-196,282-295
color domain1 red

--Eric

[phil.cruz@…]

Hi Eric,

Thanks for the quick response.  

When I first noticed this  I was mixing menu options and command lines as I was defining selectors, and had defined them using different methods and got confused with the results. The commands I sent were a way I found to reproduce it, but thanks to your explanation now I understand what happened.  Sorry to bother you.

Cheers,

Phil

On 5/26/20, 2:04 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3314: Non-functional selectors
    -----------------------------------+----------------------------
              Reporter:  phil.cruz@…   |      Owner:  Eric Pettersen
                  Type:  defect        |     Status:  closed
              Priority:  normal        |  Milestone:
             Component:  Command Line  |    Version:
            Resolution:  not a bug     |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+----------------------------
    Changes (by Eric Pettersen):

     * cc: Elaine Meng (added)
     * status:  accepted => closed
     * resolution:   => not a bug


    Comment:

     Hi Phil,
             The basic "name" command takes literally what you typed as an
     argument and remembers it, then reapplies it each time you use it.  So if
     you give "sel" as the argument then every time you use the selector you
     will get the current contents of the selection.  Conversely, the "name
     frozen" command takes its argument and finds out what it currently expands
     to and remembers that instead.  So you had two options here, either a
     series of commands like:

             select  :1-49,135-196,282-295
             name frozen domain1 sel
             color sel red

     or like:

             name domain1 :1-49,135-196,282-295
             color domain1 red

     --Eric

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3314#comment:2>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

[Eric Pettersen]

No problem. It can be confusing.

--Eric