measure symmetry helix placements wrong

[hernando.sosa@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407250342 (2024-07-25 03:42:42 UTC)
Description
measure symmetry for a helix with odd n produces the wrong symmetry matrices in one direction along the helix.  The problem is in geometry code that computes the helical symmetry matrix that must have been copied from Python 2 because it assumes n/2 is an integer.  Fix is to change that to n//2.

Log:
UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8wcm format mmcif fromDatabase pdb

8wcm title:  
NSs filament formation determines RVFV pathogenesis [more info...]  
  
Chain information for 8wcm #1  
---  
Chain | Description | UniProt  
A B | Non-structural protein NS-S | A2SZZ6_RVFV 2-265  
  

> open 37443 format ccp4 fromDatabase emdb

Opened emdb 37443 as #2, grid size 256,256,256, pixel 0.95, shown at level
0.17, step 1, values float32, fit PDB 8wcm  

> measure symmetry #2 helix 15,90,5,opt minimumCorrelation 0.95 set true

Symmetry emdb 37443: Helix, rise 14.59, angle 83.44, center 128 128 128, n 5  

> sym #1 symmetry #2

Made 5 copies for 8wcm symmetry #2  

> lighting soft




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 37 days, 18 hours, 34 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[Tom Goddard]

Fixed.

n/2 producing 2.5 for n = 5 instead of 2 using integer divide caused a 0.5 asym unit rotation.