I would agree with Clemens that the Scala GUI task generates far too
many keyworded commands, for things which have sensible defaults in
the program.
One problem conundrum for the GUI (because it works by generating a
script without actually running the program) is that the GUI has no
way of knowing what defaults are set in the program (particularly if
they are dynamic depending on the data). But this could be managed
better than it is in all cases.
Phil
On 11 May 2007, at 08:31, Clemens Vonrhein wrote:
> On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
>> The most useful aspect of the ccp4i GUI is its automatic
>> generation of
>> com files. However, I would prefer the GUI to output a .com file
>> into my
>> working directory (rather than the obscure location they are saved to
>> now) every time I run a program so that I can then tinker with it and
>> add any extra keywords I want to.
>
> I often use the GUI to get a 'second opinion' about good default
> values and options for a given CCP4 program - especially if the
> documentation is a bit confusing. Kind of double-checking if I
> understood the documentation correctly.
>
> One thing I found very confusing though, is that the com-files created
> by the CCP4i will often have (nearly) all possible keywords set, even
> if I haven't changed any of the defaults in the gui. Often, a CCP4
> program has defaults itself and only requires keywords if one wants to
> change things - which is nice, since it leads e.g. to a very short
> SCALA comand-file. I'm not always convinced that the settings done by
> the CCP4i interface (when keeping all edfaults) correspond to the
> defaults as implemented in the program itself.
>
> Maybe any parameter setting unchanged from the values in the
> $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
> the 'default value' - resulting in them _not_ being written to the
> com-file? This way any potential change in defaults inside the actual
> program would have immediate effect, even if the CCP4i hasn't been
> updated yet.
>
> Cheers
>
> Clemens
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
> * Global Phasing Ltd.
> * Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
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