Dear Bob (and anyone else interested),
1. It appears to me that the default resolution for 'isosurface
solvent' is lower for large molecules, and higher for small
molecules. Makes sense. Am I correct? Or is some other parameter also
being scaled?
2. How do I report the resolution of an isosurface? I see
'pointsPerAngstrom' in the long report 'show isosurface'. Can one
report just that one value?
3. The resolution affects the volume. Therefore, in order to compare
molecules of different sizes, I think one should specify a constant resolution.
In addition, the volume is affected by the default spacefill radii.
In models without hydrogen, the default carbon radius is 1.95 A
(unity radius, to account for the missing hydrogen). In models with
even a single hydrogen, the default carbon radius is 1.7, the vdw
radius. All good, but the isosurface volume varies accordingly. 'set
defaultvdw babel' precludes isosurfaces from using the unity radii.
Therefore, for a valid comparison of densities of non-hydrogen
non-solvent atoms per unit volume, for different molecules (some with
and some without hydrogen), I conclude this would be suitable (the
resolution value being arbitrary, but must be set the same for all molecules):
set defaultvdw babel
isosurface resolution 1.0 ignore {hydrogen} solvent volume
Do you agree?
4. At low resolution, the surface has holes, and looking through
these holes, inside the main surface one can see scraps of surface
not connected to the main surface. Also the main surface is quite far
outside the vdw surface of the molecule. This occurs by default for
very large assemblies. An extreme example for a medium-sized molecule
is generated thus:
load =7ahl
isosurface resolution 0.1 solvent
Any comments?
Best regards, Eric
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