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.)

To begin

Start with a REFINEMENT example (e.g. refmac) - at Sheffield Liz used dm because the output could be piped to O. She makes the following comments:

``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:
LHS
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
Middle
is a window showing the JOBS that have been run 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
RHS
list of other tools eg rerunning jobs, notebook etc
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

Task Window

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 job.

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).

To recap:

  1. Start from the top and work down the window.
  2. 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:

  1. 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).

  2. 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:

  1. View the log: i.e. contents of the logfile in a built-in text browser
    Nb: html log files will be displayed in a html browser (netscape)

  2. View log-graphs: this will bring up the loggraph program (replacement for xloggraph)
    This has options to manipulate graph appearance etc, and to preview and produce hard copies.

  3. 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 necessary.

Help Facilities:

  • 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 when 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.

Other features

  • 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 printers

  • "Plug in" concept, so that when viewing files the interface will choose the correct viewing program automatically.

At this point you can point people to the tutorials - if you are at a site which is going to using the interface.