On 25/02/2026 12:13, Kikuti Carlos wrote:
Hey guys, Paul,
I don't know if you are aware of the trouble Coot-1 has with rotamer and other
validation graphs: the residue numbers on the abscissa seem to ignore the
sequence gaps. The columns are associated with the PDB numbering and not the
numbers in the abscissa, and I believe the scale of the columns is not right,
or I just can't spot the problems using it because it's too pessimistic. Plus:
is green bad, and red good?
This is on m ylist. I will bump it to the top, so that I will look at it
in the next few days.
How is the Edit Chi Angles button supposed to work? A window opens up but I
can't modify anything.
You are not alone in being confused by this.
You are supposed to click on the chi-angle button in the Edit Chi Angles
dialog. This will put the mouse into "rotate chi angle" mode - so now
just go back to the graphics window and click and drag as you used to.
The 'Save coordinates' function never remembers the last folder I used, so I
keep a Finder window open there, to drag-and-drop the file name, then modify it
by hand before saving. At least we have drag-and-drop! Just a bit annoying.
Fixed in 1.1.20 (or is that what you are using?)
I save frequently because of the sudden crashes (just had another one).
Ctrl-S is "Quick Save As" (for the record).
The chain-to-chain navigation bug has been fixed in HEAD and will be
available in the next release.
(maybe related:) Oh I can't start coot-1.app from the command line, by the way.
Permission denied. It works from Spotlight, so it opens from my Home folder I guess. I am
a bit fed up with these "permissions" that Mac OS asks me to grant to programs
all the time. Maybe that is causing the issue? I can't find a way to grant access to
entire disk to Coot, if that could help.
I don't know much about Macs.
Graphics are much nicer now, could we have more options for colors of the bonds?
You have options - unless you want to change the colours of the
non-carbon atoms.
You can use
import coot
coot.set_use_grey_carbons_for_molecule(0,1)
coot.set_grey_carbon_colour(0, 0.4, 0.5, 0.6) # or whatever shade you like
Do you want more?
Graphics in Moorhen are also great, but Moorhen is still too problematic with
display bugs - I can make a video showing this, if you are interested.
Yes please.
Generally we talk about moorhen here:
https://github.com/moorhen-coot/Moorhen/issues
but happy to talk here if you don't want to do github.
Coot-1 still works fine with other functions, I still love the sphere refine
which is not available in the 0.9 series,
Click right-mouse on the right-hand side of the vertical divider in the
horizontal tool-bar. Several functions can be enabled from there
including Sphere Refine.
so I'm considering installing a virtual machine with Linux hoping to be more
efficient.
I don't follow, but it doesn't matter.
Downgrading Mac OS is not an option given institutional obligations and my
other programs.
So I hear.
Of course Coot is still the best by far, so I'm just listing the trouble hoping
that you find time to fix them. Let me know if I can help with logs and stuff
(please tell me exactly which stuff).
Well, the version that you're using is a good start. Here's my blog post
about reporting a bug in Coot or elsewhere:
https://pemsley.github.io/coot/blog/2020/09/21/how-to-make-a-bug-report.html
Paul
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