[ghemical-devel] CML file format and unspecified units

[Rzepa, Henry]

>On Mon, 21 Aug 2006, Rob Schellhorn wrote:
>
>>In Ghemical you can import CML files. Those files don't necessarily 
>>have a unit specified, as is the case with the files I feed 
>>Ghemical. Still Ghemical applies a scale factor of 10, which makes 
>>no sense. I corresponded this problem with Egon Willighagen and he 
>>suggested to scale the model in such a way that the average bond 
>>length becomes 15nm (C-C length). Can you confirm this behavior of 
>>Ghemical and what do you think of our workaround?
>
>Hello,
>
>all the file import/export features in ghemical are in fact 
>implemented in OpenBabel. So it is possible that this issue is a 
>more general one, and is related to OpenBabel.
>
>Geoff and other OpenBabel developers, what do you think about this?


CML can and should declare units, but in the case of coordinates, the 
default is normally
well behaved.

Thus if  CML declares 2D coordinates, these in fact can be any 
arbitrary unit because
they are assumed to be  "screen display units".  they probably are 
not angstroms.
If CML declares 3D units, these DO default to angstroms.

I think with 2D units, its very much up to the display software to 
normalise the
units to the screen. Multiplying by a constant factor of  10 actually 
makes no sense,
because each set of  "screen units"  may differ enormously in their scaling.
-- 

Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); 
rzepahs at mac.com (iChat)
  http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College 
London, SW7  2AZ, UK.

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