Demoing CCP4I - some notes
Peter Briggs March 1999
Before you start
It is a Good IdeaTM to
- Clear all unused windows from the screen before the demo.
- Set the font sizes to something larger.
(Use the configure interface option and the font folder at the
bottom of the window.)
Start with a REFINEMENT example (e.g. refmac) - at Sheffield
Liz used dm because the output could be piped to O. She makes the
``It really is nice if you can do something with the graphics eg O. With DM
showing the before and after map is nice. At least choose the option to
generate the map and then show the O command script.''
Then go through the interface as follows:
The Main Window
Bring this up by typing "ccp4i" and then go through:
- this has the list of PROGRAM MODULES
each module being one stage in the
crystallographic process e.g. data reduction etc
The modules are made up of TASKS
- is a window showing the JOBS that have been
The interface keeps a record of each job, whether
it suceeded, what parameters were used etc and
allows jobs to be rerun
NB: a job is a specific run of a task
- list of other tools eg rerunning jobs,
Return to this later.
Go to an individual task (eg Dm)
There is one window for each task, which contains
everything that you should need to run that task.
The important stuff should be at the top, so the rule is:
WORK FROM THE TOP DOWN
The task window is divided into "folders":
- PROTOCOL folder (at the top)
- this contains the key decisions, and choices
made here may affect the rest of the window
This also contains a slot to enter a JOB TITLE
which is displayed by the interface in the main
window and helps distinguish between different
runs e.g. of REFMAC
- FILE INPUT folder
- names of input and output files
If mtz files are input then the interface will
automatically pick up information such as column
names, resolution limits, cell dimensions or
spacegroup, and use these to set default
parameters for the task.
There is a file browser facility
- Other visible folders
- contain parameters that
should really be set by the user before running the
- Other options are in hidden folders
- these are optional
or special features which are not used for most runs
Note that any input boxes appearing in ORANGE tell the
user that this input is compulsory. The interface also
does some checking that the input is not complete nonsense
(e.g. solvent fraction must be less than 1).
- Start from the top and work down the window.
- Only visible things are important.
Start the job running
While it is running you will need to talk to pass the time until it is
finished. Liz suggests:
- Explain that the job could also have been run automatically on a remote
machine, or submitted to a batch queue (if this has been set up appropriately
for the current site).
- Draw attention to the top line in the job window. It is possible to view the
log file whilst the job is running; jobs can also be killed in the middle of a
run (there is a button to do this).
Each run saves the parameters to the database (so that it
can be rerun)
When the job has finished you can view the files:
- View the log: i.e. contents of the logfile in a
Nb: html log files will be displayed in a html
- View log-graphs: this will bring up the
program (replacement for xloggraph)
This has options to manipulate graph appearance
etc, and to preview and produce hard copies.
- View other files: e.g. mtz files. The interface
will bring up an appropriate viewer.
You can also view the command script e.g. for DM to check that it's
working okay (for users of scripts presumably). This should not usually be
- Click on the help button in the main window takes you to
the main help page. The interface automatically brings up
your browser so you can view it.
- Click on the help button in the task window goes to
appropriate help on that task (program documentation),
and RH mouse click over a particular button, input box etc
(generally referred to as a "widget") will go to specific
help on that function.
- There are also messages at the top of the task window
the cursor goes over different widgets, giving brief help
including the old keyword that function.
At this point you need to check for audience reaction before
going on to the next stage.
- Project directories and file structure
- The feedback button for comments - pointing out that
at this stage feedback is very welcome!
- Notebook facility - allows the user to record comments
on each job for later reference. There is also a
"report external program" option to record
comments on the use of a non-CCP4 program.
- Built-in configuration facility e.g. for setting up
- "Plug in" concept, so that when viewing files the
interface will choose the correct viewing program
At this point you can point people to the tutorials - if you are at a
site which is going to using the interface.