Subject: Claim for unifying

From: Laurence Cuffe <[email-masked]>
Date: Thu, 10 Feb 2000 12:39:56 +0000

I think a lot of the discussion previously in this list on a standard for 
output files is relevant here. 
As I see it chemists do a lot of different things with molecules and 
the diversity of programs and packages reflects this.  This was 
brought home to me after down loading a molecular viewer program 
which was recommended as being good for small molecules. I was 
interested in a range of four atom species at the time.  The 
program performed abysmally.  It seems that for some chemists 
"small" is molecules in or around 10 kilo daltons. 
If a feature of an interface is good and intuitive it tends to be widely 
copied.  Maybe our position as users should be to discourage the 
copywrighting of interface features which is one cause of the 
diversity in program front ends.  
One way of doing this might be to put some set of GUI standards 
in the public domain for molecular manipulation.  Another might be 
to encourage the interchangability of file formats so that you could 
use your favourite editor to build molecular descriptions and then 
export the calculation to your favourite back end program for 
computation.  In this respect I like jaguar because it reads many 
file formats for input and dislike spartan because it doesn't.  I am 
amused by gausview which will read g94 files but flattens my g98 
results like pancakes! 
  my two cents
Larry Cuffe

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From: Alain Borel <[email-masked]>
Date: Thu, 10 Feb 2000 14:43:33 +0100 (MET)

> diversity in program front ends.
Diversity of front-ends is (I think) a good thing: what would you
think if you had to use a program designed for proteins only to
study an 8-atoms coordination complex?
Different programs should serve different purposes IMHO...
On the other hand I agree that copyrighting an interface is
silly. Where would we be now if Xerox had set exclusive rights
on mice/windows/etc. ?
  
> in the public domain for molecular manipulation.
Possibly. And then everyone could write his own plugin to perform
some specific task... sounds like a good idea to me.

>  Another might be 
> file formats for input and dislike spartan because it doesn't.
Define "file formats" here: structure (PDB, XYZ...)? That's what
Babel is for :-)
Molecular dynamics trajectories? Quantum calculation results?
Usually the program includes enough documentation to transform
your data into a more suitable form. If not, then maybe complaining 
to the vendor will bring them to change their ways (especially if
the threat of losing customers becomes real enough)

>  I am 
I'm sure someone must working on it :-)

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Alain Borel <[email-masked]>     Year  2000: not the 21st century
Date: 10-Feb-00 Time: 14:32:28