This page lists known issues running CCP-EM on particular operating systems. For issues with Doppio, check out the Troubleshooting page.
Installation on Ubuntu 19+ or Fedora 29+
The following error is seen trying to run CCP-EM on some recent Linux versions such as Ubuntu 19 and Fedora 29:
ImportError: .../libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
This can be fixed by running the following command:
rm $CCPEM/lib/libfreetype.so*
CCP4 can be affected by similar issues. If you still see such errors after trying the command above, run the command again but replace $CCPEM with $CCP4.
Installation on Mac OS X 12 (Monterey), 13 (Ventura) and 14 (Sonoma)
Gatekeeper problems
Some users report problems caused by the OS X Gatekeeper. This can cause a number of different errors. On install please run the following commands:
tar xvf ccpem-20221108-macosx-x86_64.tar.gz
sudo xattr -rc ccpem-20221108
cd ccpem-20221108
./install_ccpem.sh
source setup_ccpem.sh
ccpem
Installation on Mac OS X 10.15 (Catalina) and 11 (Big Sur)
Gatekeeper problems
Some users report problems caused by the OS X Gatekeeper. This can cause a number of different errors including the following:
... cannot be opened because the developer cannot be verified. macOS cannot verify that this app is free from malware.
or:
ImportError: ... code signature in (...) not valid for use in process using Library Validation: library load disallowed by system policy
In some cases these problems can be fixed by running the following command:
xattr -rc $CCPEM
(Note: if you used sudo to install CCP-EM, you will need to use sudo to run this xattr command too.)
If that fails, please contact us. As a last resort, you could also consider disabling the Gatekeeper.
Blank RELION GUI on Big Sur
On Mac OS 11 (Big Sur), all RELION GUI windows appear completely blank. This is a compatibility problem with the version of the underlying FLTK library that was used for CCP-EM 1.5.0. More recent nightly builds of CCP-EM should not suffer from this problem because they use an updated version of FLTK.
Remote X forwarding problem with XQuartz
If you use the latest stable version of XQuartz (2.7.11 or 2.8) to connect to a remote X server (for example logging into a remote Linux system), launching CCP-EM graphical programs can fail with an error like the following:
Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
(Details: serial 322 error_code 2 request_code 149 minor_code 3)
As discussed here on the Coot mailing list, the solution is to enable indirect GLX rendering, which is disabled by default in newer XQuartz versions. Run the following command, then completely quit XQuartz (force quit if necessary). Next time you start XQuartz, X forwarding should work correctly.
For XQuartz 2.7.11: defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
For XQuartz 2.8: defaults write org.xquartz.X11 enable_iglx -bool true