Dear Herman,
On 22 Jul 2015, at 07:22, [log in to unmask] wrote:
> -This level is often specified as sigma, and here is where the difficulty gets in: Coot and Pymol will determine themselves what the sigma level of the map is, but apparently, they do it differently, so the same map, contoured at say 1.5 sigma, will look differently in Pymol and in Coot. It would be good if somebody (the developers?) could look into this.
I recently added some information to this PyMOLWiki page:
http://pymolwiki.org/index.php/Normalize_ccp4_maps
The difference between PyMOL's and Coot's normalization is:
"Normalization is done on the raw data array, not across the unit cell."
This is all you need to know to prepare or handle your data correctly (e.g. generate maps which exactly fill the unit cell, or don't normalize but specify the level in e/A^3). Whether PyMOL's defaults are good is open for discussion.
Cheers,
Thomas
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Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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