Dear CCP4bb,
The intention with CCP4i GUIs is that those folders which are open by
default (after you have chosen the mode of action from the top protocol
folder) are for everyone and those that are closed by default are for
experts OR difficult cases. Unfortunately that is an OR not an AND; the
crystal fairies are not especially kind to students. I usually suggest
that newcomers to a particular program should at least make sure they
understand the options in the open folders before running the program.
Even within individual folders we try to put the regular stuff at the top.
Ideally, I think program developers, rather than users or CCP4i
maintainers, should suggest which options to put on the GUI and which
'advanced' options to leave off. Then when you say you are using
non-GUI options we will be sure that you are boasting and not
complaining (-;.
Liz
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
