Hi Vlad The issue with the old version of Coot on Mac after updating to macOS Tahoe (v26) is a known bug.. It is probably an issue with XQuartz. However, it is now almost three years old, with no updates on GitHub for two years. I don’t know if a new release will fix this issue (or an update from Apple).
The solution is to use Coot 1 now on macOS. The density map not centering is also an issue that can be easily solved: Draw / Shader settings / and select Fancy. Regarding automatic loading (maps/coordinates), this feature is not yet implemented in Phenix. It is probably the same in CCP4i. The Coot 1 requires a brief learning phase, but it does the job exceptionally well. Some options are still missing, but Paul is working on them. We need to be patient. Cheers Xav > Le 7 oct. 2025 à 20:40, Vladyslav Yadrykhinsky > <[email protected]> a écrit : > > Hello, > > I was wondering if any of you have encountered similar issues, and how you > resolve them? > > I have recently updated my macOS, and after this, I could not run coot from > ccp4i2. > The mistakes I was getting were: > > 1. -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 > > 2. ------ Coot crashed - trying to diagnose ----- No core file found. No > debugging > > > After some attempts to fix it (including re-installing both CCP4 and XQuartz) > I have set ccp4i2 to use coot-1 instead. > > However, if it is called from the GUI from the previous job (Refmac) it shows > that it has selected the coordinates, maps, etc., but when coot-1 opens, it > has nothing. > I have to manually load everything, and then for some reason, the electron > density map is centered on the top right corner, even if I open it in > full-screen mode (screenshot attached). > > Ideally, I would like to go back to Coot. Setting up the automatic loading of > maps and coordinates would be nice. At the bare minimum, I would like the map > to be centered in the middle of the screen. > > If you had any of these similar issues, please let me know how you have > resolved them! > > Best regards, > Vladyslav Yadrykhinsky > PhD-candidate > University of Bergen > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
