The difference map has a certain predefined resolution because it is from
discrete experimental data. You cannot improve upon it. Any smoothing would be
inappropriate.
Robert M. Hanson
Chair, Chemistry
from my Windows phone
-----Original Message-----
From: "Frieda Reichsman" <frieda...@mac.com>
Sent: 1/30/2016 9:08 AM
To: "Jmol Users" <jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] isosurface mesh resolution question
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 <hans...@stolaf.edu> 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 <frieda...@mac.com> 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
USA
00 +1 413-320-7449
//////////////////////////////////////
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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
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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