Notes with markers/blobs

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC)
Description
(Suggestion arising from presentation in the CCP4 study weekend)

Would be really nice to have a system to associate user notes with a point in space - e.g. to note down speculations about the identity of a particular blob of density. Perhaps could be an extension on the Markers system?

OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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[Tom Goddard]

The current Marker toolbar lets you place a marker on a blob of density which is selected when it is created. And the label command can be used to add a note to it, for example,

label sel text "Maybe water?"

Maybe you would want some kind of GUI panel where you could just type in the label so you don't need to know the command. ISOLDE could easily add such a "Marker Note" tool -- seems most useful to people doing the refinement and building that is done in ISOLDE. A standalone capability would be fine too -- could even have a button in the Marker toolbar "Label" to bring up that tool which just has an entry field.

[Tristan Croll]

The idea here wasn’t so much a label, but the ability to attach essentially an arbitrary-length free-text document. Selecting it and then doing a command like “marker note” would launch a text editor, where the user could lay things out in more detail - e.g. arguments and evidence for or against a particular interpretation. A marker with a note would need to take on some special appearance to indicate the note’s presence.

[Tom Goddard]

Ok, so you don't care about seeing the notes in the 3D graphics. But I think most uses of notes on markers would benefit from optionally showing them in the graphics as a label. Our older Chimera program had a text entry field in the Volume Tracer gui which is the equivalent of the ChimeraX markers capability. Having a multiline input field instead of a single line is a trivial difference, although the 3D graphics labels currently don't use newline characters to show multiple lines (they should in the future, there is a ticket for that).

I am not sure about the "launch a text editor" suggestion. That seems pretty heavy-weight (and not likely to get much use), but maybe simply a gui with a multi-line text edit would do the job instead of what I proposed before of a single-line text entry field.

I still suggest that this capability is useful for very special use cases so it probably should be part of ISOLDE if that is the use case. The marker labels have been in Chimera for maybe 15 years, and for the ~6 years of the existence of ChimeraX no one has requested them in ChimeraX that I can recall. So it is not one of the heavily used missing features.