Eric, it looks like the sigma values associated with Pymol are just 1/2 the
default cutoffs of Jmol. So, for example, the one you say has 0.75 for the
best fit has a default Jmol cutoff of 1.4803, and the one with best fit 0.33
has a default Jmol cutoff of 0.67.
Maybe Thomas can explain how sigma is related in this way. What we can do is
create a new sigma parameter for the Jmol isosurface command that will match
Pymol's sigma -- at least for (some) ccp4 files. Worth a shot.
Bob
On Sun, Feb 21, 2010 at 10:09 PM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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