[MMTK] Re: Finding accessible surface area of atoms/residues in proteins

[Peter]

> > I was wondering if anyone has tried to use MMTK to calculate
> > the (solvent) accessible surface area of atoms/residues in a
> > protein loaded from a PDB file.
>
> Look at the module MMTK.MolecularSurface! 

Thanks Konrad - it looks like I should be able to do something similar with this module, but I have had some trouble with this as MMTK.MolecularSurface (MMTK 2.4.1) doesn't seem to pass its all its self tests, e.g:

c:\Python23\python.exe MolecularSurface.py -f insulin.pdb

The -f argument calls the findContacts method, and seems to do something sensible, giving following (with the water warning repeated many times):

Warning: 2 atom(s) in water were not assigned (new) positions.
6 contacts
Contact(Atom ..His10.sidechain.C_delta_2, Atom ZN.ZN)              3.09
Contact(Atom ..His10.sidechain.C_epsilon_1, Atom ZN.ZN)            3.02
Contact(Atom ..His10.sidechain.N_epsilon_2, Atom ZN.ZN)            2.11
Contact(Atom ..His10.sidechain.C_epsilon_1, Atom ZN.ZN)            3.02
Contact(Atom ..His10.sidechain.N_epsilon_2, Atom ZN.ZN)            2.11
Contact(Atom ..His10.sidechain.C_delta_2, Atom ZN.ZN)              3.09

The -v argument calls the surfaceAndVolume method, and fails:

Warning: 2 atom(s) in water were not assigned (new) positions.
Traceback (most recent call last):
  File "MolecularSurface.py", line 170, in ?
    (a, v) = target.surfaceAndVolume()
AttributeError: Collection instance has no attribute 'surfaceAndVolume'


The -a argument calls the surfaceAtoms method, and fails:

Warning: 2 atom(s) in water were not assigned (new) positions.
Traceback (most recent call last):
  File "MolecularSurface.py", line 174, in ?
    smap = target.surfaceAtoms(probe_radius = 1.4*Units.Ang)
AttributeError: Collection instance has no attribute 'surfaceAtoms'


The -p argument calls the surfacePointsAndGradients method, and also fails:

Warning: 2 atom(s) in water were not assigned (new) positions.
Traceback (most recent call last):
  File "MolecularSurface.py", line 177, in ?
    smap = target.surfacePointsAndGradients(probe_radius = 1.4*Units.Ang)
AttributeError: Collection instance has no attribute 'surfacePointsAndGradients'


Any ideas?

Thanks

Peter

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