Hey guys, Paul, I've been using Coot-1.1.19 on my Mac (switched to Mac Studio super-top-ultra-magnific after Paul told me to, also running Tahoe, in FRENCH otherwise MS Excel will mess up my budget tables - not sure the language of the OS changes anything for Coot?).
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? How is the Edit Chi Angles button supposed to work? A window opens up but I can't modify anything. 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. I save frequently because of the sudden crashes (just had another one). (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. Graphics are much nicer now, could we have more options for colors of the bonds? 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. Coot-1 still works fine with other functions, I still love the sphere refine which is not available in the 0.9 series, so I'm considering installing a virtual machine with Linux hoping to be more efficient. Downgrading Mac OS is not an option given institutional obligations and my other programs. 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). All the best! --------------------------------------------------- Carlos KIKUTI, PhD Structural Motility Team UMR144 - CNRS - Institut Curie 12 rue Lhomond - 75005 Paris, France [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> Le 25/02/2026 09:50, « CCP4 bulletin board au nom de Paul Emsley » <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> au nom de [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> a écrit : On 24/02/2026 20:03, Julie Bouckaert wrote: > Dear CCP4 bulletin board > > I accidentally upgraded to MacOS Tahoe and although with a recent > installation of CCP4-9.0.011 I can run refmac5, the graphics briefly pop up > but then disappear for good. Which is a pitty because a lot of new validation > tools, besides Molprobity, should show up. > > An error appears in red, like Error in wrapper, but then this also disappears. > > For running Coot (0.9) it says -ERROR- Ccoot_rebuild:56 Error in wrapper > coot_rebuild 0.0:: External process exited with exit code != 0 > Process: coot > -ERROR- Ccoot_rebuild:47 Error in wrapper coot_rebuild 0.0:: Error in > checking external process after completion > exit status and code: 0 1 > > Is there a solution available? - downgrade to Sequoia/Sonoma? - an adapted > plugin/wrapper? - another CCP4 package and re-install -reset parameters/paths? > > Thank you in advance for your help The problem was that Apple introduced an incompatibility with XQuartz in Tahoe https://github.com/XQuartz/XQuartz/issues <https://github.com/XQuartz/XQuartz/issues> <https://github.com/XQuartz/XQuartz/issues> <https://github.com/XQuartz/XQuartz/issues>> It may be that Coot resizes on startup and thus runs into the issues like other applications: https://github.com/XQuartz/XQuartz/issues/438 <https://github.com/XQuartz/XQuartz/issues/438> <https://github.com/XQuartz/XQuartz/issues/438> <https://github.com/XQuartz/XQuartz/issues/438>> The current solutions seem to be reinstall Sequoia 15.7.4 or Run a virtual machine with Rosetta virtualization or Use Coot 1.1.19 (I think that's what CCP4 currently distribute) (it's an option in the installer) 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 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&amp;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/ <https://www.jiscmail.ac.uk/policyandsecurity/> <https://www.jiscmail.ac.uk/policyandsecurity/> <https://www.jiscmail.ac.uk/policyandsecurity/>> ######################################################################## 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/
