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
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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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
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> 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
------------------------------------------------------------------------------
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
_______________________________________________
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