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:
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 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/
