specifying nonexistent fasta file to "rna model" gives traceback

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202006230628 (2020-06-23 06:28:47 UTC)
Description
specifying nonexistent fasta file to "rna model" gives traceback

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

executed startup.cxc  
UCSF ChimeraX version: 1.1.dev202006230628 (2020-06-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> rna path stash/pairings.txt length 100

> rna model hiv-pNL4-3.fasta #1 startSequence 455

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 263, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/rna_layout/rna_command.py", line 139, in rna_model  
mol = RL.rna_atomic_model(session, seq, base_placements, name)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/rna_layout/rna_layout.py", line 1102, in rna_atomic_model  
mol = place_residues(session, base_placements, sequence, res_templates)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/rna_layout/rna_layout.py", line 892, in place_residues  
rprev = rlist[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/rna_layout/rna_layout.py", line 892, in place_residues  
rprev = rlist[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.19
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 198.0.0.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G5033)
      Kernel Version: Darwin 18.7.0
      Time since boot: 9:26

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      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

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

[Tom Goddard]

Fixed.

Now gives clear error message if sequence file is missing or sequence string uses characters beyond a,c,g,u,t