[MMTK] Calculation of Molecular Surface

khinsen at cea.fr khinsen at cea.fr
Thu Jun 23 14:39:18 CEST 2005


On Jun 23, 2005, at 0:50, mkseo wrote:

> I am trying to calculate molecular surface of protein.
> I loaded PDB file, made protein object and calculate molecular surface 
> using surfaceAndVolume() as follows:
>
> universe.protein.surfaceAndVolume()
>
> I got error "AttributeErro: 'Nontype' object has no attribute 
> 'srufaceAndvolume'
> What is this about?

The correct usage is

	from MMTK.MolecularSurface import surfaceAndVolume
	surfaceAndVolume(universe.protein)

The error message you get is a bit misleading, it is a consequence of 
the attribute lookup rules in MMTK objects. If the attribute is not 
found in the object itself, it is searched in its type object. However, 
only objects with a database template have a non-None type object. For 
proteins, the type object is None, which is why you get that particular 
error message.

Konrad.
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