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On 04/12/2013 06:03 PM, Nat Echols wrote:
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On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan <[log in to unmask]> wrote:
Whichever way the input file for the run is prepared (via GUI or command line), anybody who doesn't inspect the log file at the end of the run is doomed and bound to commit senseless errors. I was taught a long time ago that computers always do what you told them to do and not what you think you told them, which is why inspecting the log file helps.

I agree in principle - I would not advocate that anyone (*especially* novices) run crystallography software as a "black box".  However, whether or not a program constitutes a black box has nothing to do whether it runs in a GUI or not.  The one advantage a GUI has is the ability to convey inherently graphical information (plots, etc.).  That it is still necessary to inspect the log file(s) carefully reflects the design of the underlying programs; ideally any and all essential feedback should also be displayed in the GUI (if one exists).  Obviously there is still much work to be done here.

-Nat

It is hard to blame "novices" for running crystallography software as a black box when the websites from which they download the said software use the word "automated" to describe it.  Because, at least according to wikipedia (another great resource that should be used with care), "automation is the operation of machinery without human supervision".  Checking the log-files or messages supplied by GUI seems to fall under "human supervision", which "automated" programmes should not really require.  I am not advocating return to the stone age when naming a tutorial for a widely used model building software "... for morons" was probably considered a joke (not a good one too).  I am just saying that it is perhaps quite predictable that with promise of automation comes the expectation of, well, automation.  Whether the true automation of crystallographic structure determination may become available in the future is perhaps debatable.  Whether it is already available probably isn't.

On a broader question of GUI versus command line, both obviously have their uses.  Mastering command line gives one flexibility and perhaps greater insight into what programmes actually do.  Do I prefer a little button that opens a file chooser dialog over sam-atom-in?  Absolutely.  But I am glad that --pdb and --auto command line options are supplied, because I can then write a little bash pipeline to pass 50 expected protein-ligand complex datasets through simple refmac-coot cycle to quickly see which ones are interesting.  In that regard, both ccp4 and phenix are doing it the right way - gui is simply a gateway to the command-line controlled code. I can then choose the interface that fits particular situation.

As for the relatively new CCP4 update feature, it is absolutely awesome.

Cheers,

Ed.



-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                                Julian, King of Lemurs