Hi Bob,
I tried getting just the negative difference map using
isosurface id ~m00 rmsd -2.5 within 2.5 {~retset2} insideout
"../maps/250u-2m-0.00.ccp4”
which I think is what you are suggesting below.
The negative-only difference map should be a subset of the densities seen on
the negative and positive density map, of course — that is, one should see the
negative densities only. However the resulting map is very different. It has
many more areas, and they are very chaotically arranged, so nothing like the
original map with both positive and negative.
> On Feb 2, 2016, at 6:48 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> 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.xxxSets 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 <frieda...@mac.com
> <mailto:frieda...@mac.com>> 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 <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 <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
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