Re: [Jmol-users] unused vertices in sasurface

[Robert H. <ha...@st...>]

I would check the bounds of map.dx to make sure it really spans the entire
molecule. If a surface point is outside the range of mapped data, then this
could happen because the value  will be introduced as "NaN"

Q: What does it look like at that vertex? You can use DRAW to show a dot at
that point in order to find it. Is there a hole there as well?
Q: What is the value at that vertex point?


On Sat, Jun 30, 2012 at 1:28 PM, Daniel Aioanei <aio...@gm...> wrote:

> I'm creating the sasurface of a set of atoms of the attached molecule like
> this:
>
> load 'drgfin_GMX.pqr'; select 1.OAF, 1.HAH, 1.OAA, 1.HAA, 1.OAB,
> 1.HAB; isosurface sasurface 1.4 map 'map.dx' translucent .3; zoom 40;
>
> Analysing the created isosurface I noticed that vertex number 2659
> (indexed from zero) is not used by any of the triangles. I'm
> extracting the data via the Java API: viewer.getProperty("java",
> "isosurfaceInfo", null);
>
> Is it expected to get unused vertices from time to time from the
> calculated surface, or is it possibly indicative of a potential
> problem in the surface calculation routine?
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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