On Sat, Jul 19, 2014 at 6:20 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> 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?
>
> Yes. It's set to have a 60x60x60 box as the max for default.
> 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?
>
Sort of. The points per angstrom can be different for different axes. You
should
set this your self with the isosurface RESOLUTION option:
isosurface resolution 3 ... // grid points per angstrom
>
> 3. The resolution affects the volume. Therefore, in order to compare
> molecules of different sizes, I think one should specify a constant
> resolution.
>
> absolutely.
> 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?
>
>
That looks like a reasonable thing to do. Should be easy to test -- use
set pdbAddHydrogens
true or false prior to loading and make sure the volumes are the same.
> 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?
>
This will happen when your order of detail is finer than the grid. Not much
you can do about it. If the surface has holes, the volume calculation is
not meaningful. Volume is calculated using Stokes theorem. A very nice
discussion of this is at http://brickisland.net/cs177/?p=217 A bit
technical, but it's a nice synthesis of the overall idea.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
