Mol2 type not updated

[ute.roehrig@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-79-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Hi,
When opening a mol2 file, modifying the molecule by using 'Modify Structure' from the 'Build Structure' tool, and saving a new mol2 file with the modified structure, the resulting mol2 file has the good atom names and bonds, but the atom type (and element) is not updated. See for example the attached fluorobenzene molecule, made by opening a benzene.mol2 file,  converting one hydrogen atom to fluoride, and saving the model to a new mol2 file.
Thank you for your assistance,
Ute

OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) Graphics (RKL GT1)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: Dell Inc.
Model: XPS 8940
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       4.6Gi        15Gi       857Mi        10Gi        25Gi
	Swap:          29Gi          0B        29Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4c8a] (rev 04)	
	DeviceName: Onboard - Video	
	Subsystem: Dell Device [1028:09c5]

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File attachment: fluorobenzene.mol2

fluorobenzene.mol2​

[ute.roehrig@…]

Added by email2trac

[Eric Pettersen]

ChimeraX will now not output the mol2 types from the input if it seems like the structure has been significantly modified (​https://github.com/RBVI/ChimeraX/commit/bdafe4e6edd5637f65d90275d6e2c3ff3c2a9548). Fix in next daily build.

Thanks for reporting this.

--Eric