CCP4MG Linux Known Problems

Lots of error, last line is libwhatever.so: cannot restore segment prot after reloc: Permission denied

This is caused by the "SE Linux" module of the OS. It is fixed by doing:

chcon -t texrel_shlib_t /path_to_ccp4mg_installation/ccp4mg-1.1beta4/lib/*.so

Fedora4 'missing libraries

Fails on startup complaining of missing libraries libssl.so.4 and libcrypto.so.4. To fix this make symbolic links to the libraroes which are on your system..

> cd ccp4mg/lib
> ln -s /lib/libssl.so.0.9.7f libssl.so.4
>  ln -s /lib/libcrypto.so.0.9.7f libcrypto.so.4

Graphics Drivers

When the program is started from the command line you should see the following in the window:

Loading fonts..
...DONE
Starting graphics thread..
...DONE

If the program stops after the message 'Starting graphics thread..' but before the 'DONE' then we suspect a problem with the graphics driver. We have observed that a small number of drivers need handling differently and these are listed in the file
ccp4mg/lib/GLBrokenDriver_db.py
They are not really broken just differently initialised. It is worth trying adding the info for your machine to this list following the instructions in the file.

Program Restart Status

By default the program will restart with the same data loaded. This can be switched off in the Preferences window Session tools or, if you are running the program from the command line, then use the command:
prompt> ccp4mg -norestore
These options only prevent reloading the data files from the previous session - they do not undo any Preferences. If you have problems restarting the program it may be worth trying to delete or rename the status file. The status file for the last session is
your_home_directory/.CCP4MG/status/last_exit.status.pkl

Labels and Text not Appearing - Problems with Fonts

We have observed problems with not displaying atom labels or any other text in the default startup mode. The default CCP4mg font is rendered using the Freetype font library; unfortunately this does not work on one machine that we know of. If you do not see text then please go to the Preferences (at the bottom of the Tools menu) and select the Display folder and the Fonts option. In the Fonts interface change the font for the four styles of text to one whose name starts with a lower case letter ('helvetica' is my favourite). Please inform us (ccp4mg@ccp4.ac.uk) that you had a problem and let us know your operating system, machine and graphics card.

Diagnostic Files

CCP4mg creates a directory called .CCP4MG (NB the initial dot) in the user's home area.

When CCP4mg runs (or fails to run!) it will create two files in the .CCP4MG directory: ccp4mg_stderr.txt and ccp4mg_stdout.txt. If you have problems running CCP4mg it will be a great help to us if you can email us (ccp4mg@ysbl.york.ac.uk) these files. The time and date of the program run is written to the top of ccp4mg_stdout.txt. These files will be overwritten by any subsequent program run so if the progam fails please save these files by renaming them immediately. It is common for the ccp4mg_stderr.txt file to be empty.