Save dialog mmCIF option defaults differ from saving PDB.

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10.dev202504050547 (2025-04-05 05:47:37 UTC)
Description
The save dialog mmCIF options are confusing.

When have an atomic model that I have moved to fit in a map and then save it with menu File / Save... as mmCIF format the default options save the untransformed coordinates while if I save as PDB format the default options save as the transformed (ie fit) coordinates.  This difference in default behavior is pretty confusing.

Also the mmCIF save dialog options list "Use untransformed coordinates" but don't show "Save relative to model:" while the PDB save options show "Save relative to model:".  If I have two atomic models open the mmCIF save options are different and "Use untransformed coordinates" is not present byt "Save relative to model:" appears like the PDB options.  With one atomic model and one map the mmCIF save options should show "Save relative to model:".

Log:
UCSF ChimeraX version: 1.10.dev202504050547 (2025-04-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1080 format ccp4 fromDatabase emdb

Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level
0.852, step 1, values float32  

> open 8rf4 format mmcif fromDatabase pdb

8rf4 title:  
Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit
9D4 refined against the anomalous diffraction data [more info...]  
  
Chain information for 8rf4 #2  
---  
Chain | Description | UniProt  
A | Host translation inhibitor nsp1 | R1AB_SARS2 10-126  
  
Non-standard residues in 8rf4 #2  
---  
EQT — 4-chloranyl-1~{H}-indazol-3-amine  
  
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,64.646,0,1,0,81.815,0,0,1,0

> save /Users/goddard/Desktop/test2.cif relModel #2

> open /Users/goddard/Desktop/test2.cif format mmcif

Chain information for test2.cif #3  
---  
Chain | Description  
A | Host translation inhibitor nsp1  
  
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
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: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 7 days, 3 hours, 36 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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