Xquartz reinstall works for me, but the CCP4 updater is broken. At the "Applying changes" step it will seem to pause (although using 100% of a cpu) and will continue to run despite exiting. Forced quit is needed (but doesn't seem to do any harm).
Peter ( I am very bad at monitoring this account, please use my university email address if you want to contact me directly) On Thu, 17 Oct 2019 at 09:24, Charles Ballard - UKRI STFC < charles.ball...@stfc.ac.uk> wrote: > Dear All > > as has been pointed out, and as per usual, OS X updates seem to remove > some of the setup for XQuartz, which will cause most X11 based apps to stop > working. It is best to re-install XQuartz. This will work for an updated > system that had CCP4 previously installed on it. We have had a few reports > of issues when installing on a fresh 10.15 machine through the CCP4 > downloads manager (tarball route still works). We are investigating. > > All the best > > Charles > > On 16 Oct 2019, at 17:42, Werther, Rachel A wrote: > > Thanks to all who gave advice. The reinstallation of XQuartz worked for > me. I was using the most updated version of XQuartz before I reinstalled > it, but as Guillaume Gaullier told me: > > “…macOS updates typically wipe out most files of your XQuartz installation > (XQuartz.app will still be where it was originally installed, but unlike > most Mac applications this one is not self-contained and has important > files under /opt/X11 that get erased by a system update). And Coot requires > XQuartz to display its window, so this is the most likely explanation for > why it would not work after a system update. > > Try reinstalling XQuartz from https://www.xquartz.org/< > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.xquartz.org_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8&m=zb3XqXe1iBKaPGEDyfZCe-uLxGJJVI0SzgY3of7iAxk&s=3FyzcByzIrl83gOdCoaiFSzE7Mbhtist6uxzCuQjIXA&e=>, > then log out and log back in (or reboot, that should do it too), and see if > Coot starts up normally.” > > Happy solving, > Rachel > > Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / > Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org<mailto: > rwert...@fredhutch.org> / 206-667-4066 > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto: > CCP4BB@JISCMAIL.AC.UK>> on behalf of "Werther, Rachel A" < > rwert...@fredhutch.org<mailto:rwert...@fredhutch.org>> > Reply-To: "Werther, Rachel A" <rwert...@fredhutch.org<mailto: > rwert...@fredhutch.org>> > Date: Tuesday, October 15, 2019 at 5:01 PM > To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" < > CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> > Subject: [ccp4bb] Issues in new Mac version 10.15 > > Hello All, > > I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t > open on my computer. > > Phenix opened as usual. I use the GUI, and the button that says “Open in > COOT” was not greyed out, but would not launch the window. When I tried to > open it directly from Finder, it also failed to open. The cartoon coot > appeared on my recently opened section of my bottom-of-screen toolbar, but > nothing happened. > > Next I downloaded the latest CCP4-7.0.077, and followed the instructions > to remove the extended attributes: > ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X > version 10.13 or later (10.12 was not tested), you will have to remove > extended attributes from the tar-gz-file before unpacking it, otherwise the > app icons will not be functional (and you will be able to launch the CCP4 > apps including ccp4i and ccp4i2 from the command line only). The extended > attributes can be removed from the file _file_ using the command "xattr -c > _file_". For example: xattr -c ccp4-7.0.065-macosx64.tar.gz > > But when I try to open CCP4, I get this message: > Ccp4 cannot be opened because of a problem. > Check with the developer to make sure ccp4 works with this version of > macOS. You may need to reinstall the application. Be sure to install any > available updates for the application and macOS. > Click Report to see more detailed information and send a report to Apple. > > And when I try to open Coot from the Finder, I again just see the icon in > my recently opened section of my bottom-of-screen toolbar, but it doesn’t > open. > > Any advice? > > Many thanks, > Rachel > > Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / > Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org<mailto: > rwert...@fredhutch.org> / 206-667-4066 > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1< > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8&m=DLlHXm0LUKHS_PFqce1iCejwGvyoaCkFpJGwuJyob_Q&s=HfIn8TsXm95kj-mZzZ_fHbCh2I6Lzu3-v2XlHisInZQ&e= > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
