Save mmCIF files with unix line endings instead of DOS line endings

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Surprisingly ChimeraX is saving mmCIF files with DOS line ending on Mac.  This seems undesirable.  The mmCIF files from the PDB have unix line endings.  This didn't cause any problem for me, only I was debugging why Foldseek web service rejected our mmCIF files and noticed that we were giving it DOS line endings.  That was not the reason Foldseek rejected it but I wasted time testing if that was the problem.

I think we should follow what the PDB does for mmCIF line endings (unix).

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8jnb format mmcif fromDatabase pdb

8jnb title:  
CRAF ras-binding domain chimera, ligand complex [more info...]  
  
Chain information for 8jnb #1  
---  
Chain | Description | UniProt  
B | RAF proto-oncogene serine/threonine-protein kinase, CRaf | RAF1_HUMAN 50-101 114-141, BRAF_HUMAN 102-113  
  
Non-standard residues in 8jnb #1  
---  
USX — 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-
phenoxy]ethanamide  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> save test.cif




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 22 days, 16 hours, 28 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    aiohttp: 3.9.5
    aioitertools: 0.11.0
    aiosignal: 1.3.1
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[Greg Couch]

Agreed. I found a commit, ceebbe884ecca01a634193df961fee0a58584aba, 28 March 2019, that said "Don't write DOS line ending in mmCIF files." But it explicitly set the line ending to "\r\n". I'm pretty sure that the comment is what the code should have done.