In my case, downSample 2 makes most of the surfaces disappear, unfortunately.
Because I am using a difference map, most of the surfaces are quite small to
begin with— maybe their small size is causing disappearance. Any other options
you can think of for smoothing small surfaces?
> On Jan 28, 2016, at 11:46 PM, Robert Hanson <[email protected]> wrote:
>
> Frieda,
>
> You cannot set the resolution of an isosurface that comes from a volume data
> file such as that using the RESOLUTION option. What you can do is use the
> DOWNSAMPLE option. What this does is to skip points in the grid. The
> RESOLUTION option is only for isosurfaces that are generated de novo by Jmol
> -- vdw, sasurface, molecular, solvent.
>
> Bob
>
>
> On Thu, Jan 28, 2016 at 8:39 PM, Frieda Reichsman <[email protected]
> <mailto:[email protected]>> wrote:
> Hi Bob,
>
> Using the following command:
>
> isosurface id ~m40 rmsd 2.0 sign red [x00dd00] within 1.5 {ret}
> "250u-2m-0.40.ccp4" resolution 5.0 mesh nofill;
>
> and trying to the resolution of the mesh to a finer level, I find no change
> in resolution from the default. I’ve tried placing “resolution 5.0” in a
> variety of different locations within the command, to no effect.
>
> Also - will red become the negative rmsd in the way I’ve set it up? Hard to
> tell from the documentation.
>
> Thanks,
> Frieda
>
>
>
> //////////////////////////////////////
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com <http://www.moleculesinmotion.com/>
> USA
> 00 +1 413-320-7449 <tel:413-320-7449>
>
> //////////////////////////////////////
>
>
>
>
>
>
>
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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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