All right! Thank you for the links, I’ll prepare the Moorhen video soon. You are right about the blog for bug report, this makes more sense than bitching by e-mail. And I might find out if someone else already noticed something similar.
I’ll just reply about the Edit Chi Angles thing, because it is not doing what you said and I checked the feedback : it does let me choose the Chi angle to change, then I go back to the model, click and drag. The terminal says it is moving the atoms, but the ghost image (the usual faint bonds showing the new position as in “Refine”) are not showing up, and when I click Accept (without knowing what I am doing, really), nothing changes. Refine and Rotamers and the others work fine, this is specific to the Edit Chi Angles feature. Then, still on Edit Chi Angles, when I check the “Use Hydrogen Atom Torsions” box, Coot crashes immediately (this is reproducible): Termination Reason: Namespace SIGNAL, Code 11, Segmentation fault: 11 Terminating Process: exc handler [48205] Another display issue with Mac OS, as you love them? Great to know some of the bugs are already being cleared, I think the Linux virtual machine will wait. Thanks! My best wishes! --------------------------------------------------- Carlos KIKUTI, PhD Structural Motility Team UMR144 - CNRS - Institut Curie 12 rue Lhomond - 75005 Paris, France [email protected]<mailto:[email protected]> De : Paul Emsley <[email protected]> Date : mercredi 25 février 2026 à 13:55 À : Kikuti Carlos <[email protected]>, "[email protected]" <[email protected]> Objet : Re: [ccp4bb] CCP4i2 in MacOS Tahoe: no wrapper, no creation of graphics in Results and problems with starting Coot 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
