mseries with negative step: NameError: name 'models' is not defined

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
mseries command with negative step option does not work.

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/Users/goddard/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/Users/goddard/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 956, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 815, in resolve  
dist = self._resolve_dist(  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 861, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Clipper 0.21.0
(/Users/goddard/Library/Application Support/ChimeraX/1.6/site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0 (/Users/goddard/Library/Application
Support/ChimeraX/1.6/site-packages), Requirement.parse('ChimeraX-
Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})  
  
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1r7z format mmcif fromDatabase pdb

1r7z title:  
NMR structure of the R(ggaggacauuccucacgggugaccgugguccucc), domain IV stem-
loop B of enteroviral ires with auuccu bulge [more info...]  
  
Chain information for 1r7z  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | 34-MER  
  

> mseries #1 step -1

Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_series/mseries.py", line 32, in mseries  
msp.start()  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_series/mseries.py", line 104, in start  
self.inext = 0 if self.step > 0 else len(models)-1  
NameError: name 'models' is not defined  
  
NameError: name 'models' is not defined  
  
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_series/mseries.py", line 104, in start  
self.inext = 0 if self.step > 0 else len(models)-1  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 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: 32 GB
      System Firmware Version: 515.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 56 days, 23 hours

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Tom Goddard]

Fixed.

The mseries code was clearly intended to work with negative step but I guess it was never tested or the code was changed then not retest. Fixed, replacing "models" with self.models.