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 / [log in to unmask]<mailto:[log in to unmask]> / 206-667-4066
From: CCP4 bulletin board <[log in to unmask]<mailto:[log in to unmask]>> on behalf of "Werther, Rachel A" <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: "Werther, Rachel A" <[log in to unmask]<mailto:[log in to unmask]>>
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>
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 / [log in to unmask]<mailto:[log in to unmask]> / 206-667-4066
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