I had one on GitHub for Chimera (chimera-trimmings)… I will make one shortly for chimerax, have just been finding my footing with it after a while using “old” chimera :)
Cheers
Oli
Hi Oli,
Do you have a webpage somewhere, where you could share all your accumulated aliases?
Cheers,
Alexis
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000”
"alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers
Oli
> On Sep 6, 2023, at 12:42 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
>
> Hi Oliver,
> The problem is that the default "target" for hide is atoms if any of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden.
> I think your options are to either specify the target as models in the hide command, or use a specifier that more directly selects maps, such as ##volume.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Hi,
>>
>> I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
>>
>> “Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
>>
>> A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
>>
>> Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
>>
>> Cheers
>> Oli
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