Re: [Jmol-users] different RMSD value for positive and negative areas

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

You can create two independent isosurfaces, one positive and one negative.
I have not tried that with difference maps, but it should work. I think it
all goes through the same algorithm.

*CUTOFF x.xxx*Sets the cutoff value defining an isosurface. Typically,
smaller values correspond to a larger object. Cutoffs can be either
positive or negative. In the case of a molecular orbital, a positive number
indicates to use both positive and negative cutoffs. Adding an explicit "+"
sign before the number indicates that only the positive part of the surface
is desired. (See also RMSD, below.)

On Tue, Feb 2, 2016 at 4:45 PM, Frieda Reichsman <fri...@ma...> wrote:

> Hi Bob,
>
> Is it possible to obtain a difference density map (isosurface) at a
> different RMSD for the positive and negative areas of the map?
>
> For example, can I specify an RMSD value of 2.0 for negative areas of the
> map, and an RMSD value of 2.5 for the positive areas?
>
> Alternatively, is it possible to make a map that is negative only?
>
> Thanks,
> Frieda
>
>
>
> //////////////////////////////////////
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> USA
>
> //////////////////////////////////////
>
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-- 
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