id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3231	Underscores in atom/residue names	goddard@…	Conrad Huang	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC)
Description
It seems that atom names with underscores are not allowed in parsing atom specs.  And yet ChimeraX reads in PDB files with such atom names.  This example I am looking at is a material science polymer so a bit weird.  But if commands can't parse underscores in atom names then we probably should give some extreme warning when opening such a file because it breaks all our commands.  Even ctrl-click to select an atom fails with a very cryptic error cdialog ""Expected objects specifier or keyword"" since the ctrl-click uses an equivalent command which uses the unparsable atom name.

I'm not going to attach the PDB file since it is private data from a researcher, but it is trivial to reproduce by editing any PDB file to put an underscore in the atom name.

Log:
UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/people/luchinsky/polymers.pdb format pdb

Summary of feedback from opening
/Users/goddard/ucsf/people/luchinsky/polymers.pdb  
---  
warnings | Cannot find consistent set of bond orders for ring system
containing atom C_4 in residue **** :53  
Cannot find consistent set of bond orders for ring system containing atom C_4
in residue **** :90  
Cannot find consistent set of bond orders for ring system containing atom C_4
in residue **** :133  
  

> select :43@H_6

Expected an objects specifier or a keyword  




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: 8 days 57 minutes

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

}}}
"	defect	closed	normal		Command Line		fixed		Tristan Croll chimera-programmers				all	ChimeraX