Removing actual altlocs doesn't update alloc models

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 UTC)
Description
If I use "altloc clean {sel}" to remove the altlocs from a residue while the altloc display is present, the altloc display for that residue is not removed and is not affected by subsequent "altloc hide" commands.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4qog

4qog title:  
Crystal structure of fad quinone reductase 2 in complex with melatonin at 1.4A
[more info...]  
  
Chain information for 4qog #1  
---  
Chain | Description | UniProt  
A B | Ribosyldihydronicotinamide dehydrogenase [quinone] | NQO2_HUMAN 0-230  
  
Non-standard residues in 4qog #1  
---  
FAD — flavin-adenine dinucleotide  
ML1 — N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide (Melatonin)  
ZN — zinc ion  
  
222 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> show

> altlocs show

> view /B:131

> altlocs clean /B:131

Removed alternate locations from 3 residues  

> altlocs hide

> close #1.2.19

> altlocs show

> select #!1/B:132@CB

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel

> show sel

> select clear

> select #!1/B:132@CB

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> altlocs clean sel

Removed alternate locations from 1 residue  




OpenGL version: 3.3.0 NVIDIA 555.85
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

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[pett]

Fixed in 1.9 daily build. Not putting it in the 1.8 rc at this late date since it changes atomic_lib (though in a link-compatible fashion AFAIK, but still).

Fix: ​https://github.com/RBVI/ChimeraX/commit/53c8e64d63ff17ed710e71072fe5632ac16d9c1b