The Database Utility maintains a record of all tasks performed in
a project. The Interface provides simple tools to archive and restore data
files, which can function as a notebook or logbook. The user can add any other
information. Thus, it is possible to keep track of a structure
determination and refinement process without using a pen and paper.
Setting up a Database for a project starts with choosing a Project directory
using the Directories&ProjectDir interface. A database directory
called CCP4_DATABASE is usually set up
as a subdirectory of the Project directory.
The Job List
The Job List window (in the centre of the Main Window of the Interface,
coloured salmon pink in the picture) is a reverse order list of all the jobs. The format of each line
in the List is:
Each job is assigned a number at run time
Date or time
Lists the start time of a running job or
the finish time. For jobs not run today the date of run is listed
The Database menu is the scrollable menu on the right-hand-side of the Main
Window, below View Any File (coloured salmon pink in the picture).
Most of the options in the menu require that one job is selected from the Job List by
clicking the left mouse button on the desired line. If more than one job is currently
selected, the action will be applied to the last selected. If no jobs are selected,
the action will be applied to the job at the top of the list. More than one job may be
selected for the option Delete/Archive Files. All job selections can be cleared using the F2 function key on your
All of the files associated with the selected job (log file and all
extant input and output files) are listed in a pop-up menu. The selected file
is displayed with
The FileViewer Utility (unless
The pop-up menu contains the following:
View LogFile in Web Browser
If the log file is in HTML format, there is the option for them to be displayed in
a web browser, including links to documentation and in-line graphs. Note that there may
be some delay as Netscape first loads the Java applet to display graphs.
View LogSummary in Web Browser
If the log file is in HTML format, the sections tagged as SUMMARY are displayed in a web
View Log File
Display log file with the FileViewer utility, regardless of the file format.
Display the command scripts for the CCP4 programs which were run for the selected job
Beware: since these are temporary files written to the scratch area ($CCP4_SCR, which
may or may not be the same as your TEMPORARY directory), they will probably not be kept
indefinitely on your computer. Also, if you run a job on a remote machine with a
different definition of $CCP4_SCR, these files may not be visible even if they do
The remainder of the pop-up menu is filled with all other input and output files
associated with the selected job.
This is a means to explicitly delete temporary files or output which
you no longer wish to keep. It is also a means to 'archive' files which
means saving a compressed version of the file to the database directory.
Note that temporary files are usually written to the TEMPORARY directory
and, depending on the setup in your lab, these may be deleted automatically
after a period.
The default cleanup level can be set in the
Preferences window. The program default
is the 'safe' option to 'Delete temporary file' but most users will probably prefer the
'Delete output files and remove from database'. If you have selected more than one job,
there is an option at the top of the window to reset the cleanup mode for all
For each of one or more jobs selected from the job list you have the
option of several levels of cleanup:
Delete temporary files
Delete the files with extension .tmp
created by the run script on the TEMPORARY area. These will be mostly input
command scripts for CCP4 programs but there may be other intermediate files.
This is the default option. This default can be changed through the
Delete all output files
As above and delete the log file and all output files.
Delete output files & remove from database
As above and remove all record of the job from the database.
The log file and any other extant output files are listed with options
to: Delete, Keep, Archive,
Retain archive, Restore archive etc.
The default option is set to either Delete or Keep,
dependent on the cleanup level chosen. This default will be overridden if you change
the option for the individual file.
Archiving a file involves saving a compressed version of the file (by
default it is compressed with the gzip utility) to the
$Project/CCP4_DATABASE directory. The archived file has the original
file name, with the extension .gz added.
If there is already an archived version of the file, options to
Retain archive (i.e. keep it, no change) or
Restore archive (uncompress and copy back to the original file
name) are present.
The Restore options in the archive include
either deleting the original file or, if not explicitly stated, the original is
The Interface will terminate the currently selected job, or the last one if
no job is explicitly selected. It will ask you to confirm that you want to kill
the job. Any running job will have one process which is running a script and probably
a child process which is the running program. The Interface will attempt to kill the
child program process but if it can not find a program process after three retries,
it will kill the script process. The Job List will show the job status as KILLED.
The Interface will kill both local and remote jobs. Whilst killing local jobs usually
takes immediate effect, you should expect some delay in killing a remote job.
This operation is very dependent on the operating system; if you have problems,
the following information may help. To kill a job, the Interface reads the header of
the log file which has the script process ID on the line commencing "#CCP4I PID".
It uses the Unix commands 'ps -l' to find the currently running processes and the
'kill -9' command to kill a process. If the attempt to kill a process fails, the
Interface should report where it has failed. If you have problems, please report
them to CCP4 or look in the script $CCP4I_top/src/local.tcl at the procedures
KillScript and KillRemoteScript.
This provides for speedy rerunning of jobs that FAILED or ones you wish
to repeat with minor changes of parameters.
Select a job from the Job List before clicking ReRun Job.
A Rerun Job window comes up. The task window(s) for the job may be reviewed
and edited before rerunning the task.
Edit Job Data
The Edit Job Data menu contains the following:
This is a means to save any comments about a job. Select a job from the Job List first.
Each job has its own notebook file in the database directory which is created when you select
Read/Edit Notebook. The file is
created with header information indicating to which job it belongs. You
should edit in your comments after the header information.
Edit Job Data
There is an option to edit the data stored
in the database. This might be useful if you rename a file and want to update the
information in the database or if you want to change (or add) a title for a job.
Enter Data for External Job
There is also an option to Enter Data for External Job
which will allow you to input information on jobs run outside the database.
For example this might be useful for recording what you did using molecular graphics.
You can record the names of input and output files and also then use the Edit Notebook
facility to write up what you did in more detail.
In order to change Interface defaults, e.g. where output files go, use
the Preferences button.
View Session Log
Each CCP4i run keeps a session log file recording only significant actions such as
jobs run and files deleted. It may also contain error diagnostics which might be useful to
the developer but probably not to the user. The log file is saved as $HOME/.CCP4/CCP4_session.log.
Each time CCP4i starts up, any existing file of that name is overwritten. The session log
file can be viewed from the Interface using the 'View Session Log File' option on the right
hand side of the Main Window.
The Interface can be configured to use different system resources such as web
browsers, printers and remote machines. Most users should not need to change
these as they should have been set up when CCP4i was installed. The one option
they may like to change is size of fonts.
A detailed description of how the Interface
can be configured to the user's preferences, can be found elsewhere.
The user can save the setup with the Save button and should
usually choose the Save to user's home directory option.
The Interface will be updated to reflect the new configuration
but it may be necessary to close and reopen a window to see the new configuration.
Edit Modules File
The Edit Modules File button gives a window to edit the modules and
task references which appear in the menus on the left-hand side of the main CCP4i
window, and which are stored in the modules.def file.
Install New Task
The Install New Task
button gives a window to copy new task definitions (from a Task source) into
the current installation. There are also options to uninstall tasks which have
previously been installed using this function.
All the database information is saved in the CCP4_DATABASE sub-directory
of the Project directory. It is kept here so that if the Project directory
is moved (between computers/labs etc.), the database is less likely
to be left behind. In this directory are:
The information in the Job List and additional information is
saved in this file when the Save Database to File
option is used. The file has the standard .def file format.
Parameter def files
For each task run the parameters are saved in a .def file.
The file name
is constructed from the job number (jobid) and the name of the
task (task), as follows: jobid_task.def
This file will be used by the ReRun Job option.
If the Save&Restore option on a task interface is used
to Save a Current Task Default, a file called taskname.def
will be saved in the database directory. This file will be used to initialise
the parameters whenever that task interface is used.
All archived files have the same name as the original file with the
extension .gz (assuming your system uses the gzip compress mechanism).
These files are accesed via the
Delete/Archive Files button.