~surf vs. surface model display

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC)
Description
If I do:

surf #1
~surf

... on a model, the surface model is still shown as displayed in the Models panel, and toggling its display checkbox there does nothing (other than delete the clip caps, if they were present). I think this is fairly recent behaviour?

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: 1.7.dev202307112022 (2023-07-11)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description | UniProt  
A | EtuB protein | A5N734_CLOK5 75-304  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> surface #1

> ~surface




OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
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]

~surf has always been an alias for "surface hidePatches", so knowing this, the behavior is unsurprising and hasn't changed in recent versions. It is kind of unfortunate how it interacts with the model-display control, but if you had a partially displayed surface that you wanted to temporarily hide, that is how you would want it to work.

Maybe a message could be issued if you turn on the model display of a surface that has all its patches hidden?

[Tom Goddard]

This is how it works in Chimera and has always worked in ChimeraX. I agree it is confusing that ~surface might mean close the surface, or hide the surface model, or hide the surface for all atoms. It does the last of those 3 which is probably the worst and least useful, but we kept it that way for compatibility with Chimera.

I suggest you don't use any "~" commands. That is a Chimera anachronism which is mostly good for confusing yourself, as in this case. Instead use the clearer, more self explanatory "surface close #1" or "surface hidePatches #1" or "hide #1 model".

[Tristan Croll]

… Huh. I have *no* idea how I didn’t notice that before.

On Mon, 17 Jul 2023 at 19:43, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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