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 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
