Actually, hold that. Not sure of this result, let me do more testing first. May
be a day or two.
> On Feb 3, 2016, at 10:46 PM, Frieda Reichsman <frieda...@mac.com> wrote:
>
> 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
>> <mailto: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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