That sounds about right.
We need to track down the definition of "sigma" that pymol is using. Jmol's
definition of "cutoff" is straightforward -- just the actual isovalue. Not
having any familiarity at all with python, I haven't been able to find this
in the Pymol code.
Perhaps someone else can spot that....
Bob
On Sun, Feb 21, 2010 at 7:59 AM, Eric Martz <[email protected]> wrote:
> OK, I misinterpreted the scaling differences in my previous report. The
> problem appears to be a simple scaling factor difference between Jmol's
> isomesh cutoff value and PyMOL's isomesh sigma value. (Contrary to my
> previous interpretation, I don't think the scaling varies from the center of
> the molecule.)
>
> However, I now notice that the scale factor (cutoff vs. sigma ratio that
> makes the two isomeshes the same) varies with the size of the molecule
> loaded.
>
> Detailed demonstrations are at the top link on this list:
> http://www.umass.edu/molvis/tests/
>
> -Eric
>
> --- On Fri, 2/19/10, Robert Hanson <[email protected]> wrote:
>
> > From: Robert Hanson <[email protected]>
> > Subject: Re: [Jmol-users] Problem w/ electron dens. maps
> > To: [email protected]
> > Date: Friday, February 19, 2010, 7:40 PM
> > Exactly the problem. We have wildly
> > different data sets -- from electron diffraction to X-ray
> > data. Where did we end up with that discussion about sigma?
> > I can certainly look at the Pymol code and see what Warren
> > did there.
> >
> >
> > Bob
> >
> > On Fri, Feb 19, 2010 at 11:37 AM,
> > Thomas Stout <[email protected]>
> > wrote:
> >
> >
> > But electron density maps can be on arbitrary scales, so
> > the value "1.0" may very well be meaningless
> > (except in the particular case where normalization has made
> > 1.0=1e-/A**3), and will certainly produce wildly different
> > results from dataset to dataset depending on the provenance
> > of each particular dataset (scale factors, etc). The
> > "standard" in macromolecular crystallography is to
> > view density maps at 1.0sigma & "difference
> > maps" at 3.0sigma.
> >
> >
> >
> > -Tom
> >
> >
> > On
> > Fri, Feb 19, 2010 at 7:49 AM, Robert Hanson <[email protected]>
> > wrote:
> >
> >
> > Eric, I think this is just that Pymol has a different
> > definition -- 1.0 sigma is not 1.0 value. Jmol uses actual
> > value 1.0, not "sigma" 1.0.
> >
> > Bob
> >
> >
> > On Fri, Feb 19, 2010 at 7:26 AM, Eric Martz <[email protected]>
> > wrote:
> >
> > Dear Bob,
> >
> >
> >
> > I'm sorry to report that Jmol 11.9.29 is not displaying
> > ccp4 electron density maps correctly as isomeshes. I have
> > demonstrated a major problem here (hopefully not major to
> > fix):
> >
> >
> >
> > http://www.umass.edu/molvis/tests/jmol_edm_test5/
> >
> >
> >
> > -Eric
> >
>
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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