|CCP4i: Graphical User Interface|
By default, when you choose to Delete/Archive Files for a job, the option is to Delete temporary files but you can change this. You will probably want to change it to Delete output files & remove from database but beware that it is then easy to delete files by mistake.
When selecting files, you can choose whether to list the files in either alphabetical order (the default) or by data type.
CCP4i will create maps in the tasks 'Generate Patterson Map' and 'Run FFT - Create Map' and optionally will create some specific maps to help review results in the tasks 'Run DM', 'Run Solomon', 'Run Refmac' and 'NCS Phased Refinement'. Maps can be created in CCP4 format or the appropriate format for the graphics programs O, Quanta or XtalView. You can set the preferred default format. By default maps are created in the TEMPORARY directory but this can be changed in the Preferences to be the current project directory. N.B. the TEMPORARY directory is usually the same as the scratch directory, as defined by the environment variable $CCP4_SCR in the CCP4 setup script, but it can be set to somewhere else in the Directories&Project Dir window.
In order for the 'Refmac5 interface to give output map names explicitly', the toggle button has to be switched on. This means that if in the Refmac5 Protocol folder the option to 'Generate weighted difference maps files in ... format' is toggled on, the Refmac5 Files folder will contain lines for the 'Fwt map' and the 'DelFwt map'.
By default CCP4i will display PDB files as text and just the header of CCP4 map files. You can choose to change the the default viewers for these two file types to a different viewer defined within the interface.
The default option is Do not create harvest file, but increasingly you should choose to automatically do data harvesting. This would mean creating a harvest file in either the project directory or the harvest directory (programs interpret this to be a subdirectory of $HARVESTHOME). Data harvesting files can be kept private, which can be set in the Preferences. There is also an option to put a maximum on the width of a row in the deposit file.
Warning: this is a developmental option!
Some tasks in CCP4i can use XML files to communicate information within the interface. This option determines whether or not this communication is turned on. The default is have it turned off, and it is not advised to use this unless you know what you are doing.
Currently the XML communication is only used between the Matthews, Analyse MR Data, and Molrep interfaces.
The Preferences window has two options for saving the preferences: either to Save to Installation File or to Save to User's Home Directory. You should only save to the installation file ($CCP4I_TOP/etc/preferences.def) if you are the system manager responsible for installing CCP4i. If you are not the system manager, you should not have write permission to this file if your system manager has set things up wisely. The alternative is to save a set of personal preferences to your $HOME/.CCP4/unix/preferences.def.