On 11/09/2026 17:18, Chip Lesburg wrote:
A few more observations and suggestions for Coot 1.x
I’m using Coot 1.x-pre b9ade0e82fa509f24ea458adf5d2939629bb73ec on
MacOS 26.6.2
1.
After deleting a water, the water is still shown until I move
away, at which point it disappears. I think it should disappear
immediately just as with residues etc.
I agree - fixed in 76db80d421c06bb4e90016ea2d9f2f1ea6f6a7d0 (as a result
of this message)
1.
I’ve mapped the “w” key to add a water at the current center,
which worked in a previous version, but now Coot crashes with the
info below in the console. Please let me know if you want
additional information.
The function needs to be in the coot namespace/module:
coot.place_typed_atom_at_pointer("Water")
if you are writing Coot python scripts, I highly recommend doing so
using an LSP. Here I am using pyright in neovim - you can see that
there's something wrong as you type it (plus, had I started with "coot."
I would get function name completions and in-line documentation).
Anyway, you have tickled a long-standing bug in Coot - trying to access
a deleted pointer to a function - sometimes it works, sometimes it
crashes. Fixed in 6a494da3148d0e4f442d05a5f858c7cea38e4fda (11th Sept.).
1.
In the delete menu, I have occasionally mis-clicked on “All
Waters” when I meant to click on just “Water”. Thankfully, the
undo mechanism came to the rescue, but I wonder if it makes any
sense to rearrange the list to put frequently-used (and
potentially less destructive) items at the top? For instance, I
typically use Water, Residue, Hydrogen Atoms in Residue, Residue
Atoms with Alt-conf, Residue Range.
I've moved "All Waters" down.
1.
I’ll reiterate the suggestion to improve the utility of the “o”
keybinding to cycle among NCS-related chains: when centered on a
non-protein (e.g. water), the “o” key does nothing. Rather, I need
to center on a nearby protein atom for the NCS cycling to work. I
would suggest that when the “o” key is hit, that the closest
protein atom is found and then the matching NCS operator is
applied to the view. I hope this makes some sense.
Yes. It sometimes happens to me. Never been at the top of the list
though. I will make a note.
1.
When looking at the list of outliers on the left side (via
Validate > Overlaps, Peptide, etc. or Validate > Validation
Outliers - is there a difference between these two menu items?),
would it be possible to add a small region to toggle on/off
certain types of outliers?
Hmm... It used to be possible to get a table for each type. Maybe I
should recreate that...
1.
When looking at lists of items (validation outliers, difference
map peaks, etc.) the contrast between selected and unselected
items is still pretty weak - could this be made a bit less subtle?
Also, it’d be useful if the arrow keys (or comma and period as in
0.9.x) could be used to move up and down in the list.
You are not the only one. Fixed in
c3d072d6f46050eb16106abe4ef86d3056c9a03a (13th Aug - so that should be
in your build... hmm).
If it's working as intended (toggle buttons, not simple buttons), then
this is a theme issue - not a Coot issue.
They look a bit subtle, distinguished in colour enough to me though.
Coot (like other GTK4 apps) inherits the highlights and accents from the
macOS.
Coot is such an amazing tool, so thank you so very much for continuing
your work on it!
Thanks.
Paul.
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