Hello Xav and Lucrezia, Thank you for the fast response. It is somehow calming to know these issues are common and not unique to me. This macOS update of mine has caused several software to stop functioning one way or another in a very deadline-tight part of my project, hence the frustration.
Xav, thank you for the advice. I opened it again to try to set the shader settings, and this time the map was centered properly, even before I could do anything. Lucrezia, thank you for the advice and the tutorials. I have also just found your and Paul's tutorial on YouTube, so I hope to catch up quite soon. Best regards, Vladyslav ________________________________ From: Vladyslav Yadrykhinsky <[email protected]> Sent: Tuesday, October 7, 2025 21:37 To: Lucrezia Catapano <[email protected]> Subject: Re: [ccp4bb] coot running issues and coot-1 interface Hello Xav and Lucrezia, Thank you for the fast response. It is somehow calming to know these issues are common and not unique to me. This macOS update of mine has caused several software to stop functioning one way or another in a very deadline-tight part of my project, hence the frustration. Xav, thank you for the advice. I opened it again to try to set the shader settings, and this time the map was centered properly, even before I could do anything. Lucrezia, thank you for the advice and the tutorials. I have also just found your and Paul's tutorial on YouTube, so I hope to catch up quite soon. Best regards, Vladyslav ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Lucrezia Catapano <[email protected]> Sent: Tuesday, October 7, 2025 21:29 To: [email protected] <[email protected]> Subject: Re: [ccp4bb] coot running issues and coot-1 interface Hi Vlad, Try: Draw-> View- >Scale up/down Graphics. It should resolve the issue. As Xavier said coot 1 requires some practice. I made some tutorials available here: mrc-lmb.cam.ac.uk<https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/tutorial.html> [favicon.ico]<https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/tutorial.html> Best, Lucrezia Lucrezia Catapano, PhD (she/her) Postdoctoral Scientist Murshudov Group MRC Laboratory of Molecular Biology Francis Crick Avenue, Biomedical Campus, Cambridge CB2 0QH, UK. On 7 Oct 2025, at 20:09, Xavier Brazzolotto <[email protected]> wrote: CAUTION: This email originated from outside of the LMB: [email protected]<mailto:[email protected]>-. Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to [email protected]<mailto:[email protected]> -- 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]<mailto:[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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [External email] Make sure you recognize the sender's email address before you click links, open attachments, or get involved in financial transactions. Contact IT-support BRITA if you have any questions. ######################################################################## 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/
