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
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
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>
>
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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http://p.sf.net/sfu/intel-sw-dev
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