I will try and track down the actual algorithm used - CCP4, O, PyMOL,
MAPMAN, XPLOR/CNS, SOLVE and Phenix (and others) all read and/or write
electron density maps with the same understanding of "sigma" levels,
so it is well standardized in the field. I'm fairly certain that it is
just RMSD but will need to confirm that... If -- in the map that you
and Eric are looking at -- 1 rmsd happens to correspond to the mean,
would that account for the factor of 2 if you are using "mean +
rmsd*sigma"?
-Tom
Sent from a tiny virtual keyboard.
On Feb 21, 2010, at 8:56 PM, Robert Hanson <[email protected]> wrote:
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
>
---
---
---
---------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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
---
---
---
---------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
