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One cannot understand what is going on without knowing how this map
was calculated. Maps calculated by the Electron Density Server have
density in units of electron/A^3 if I recall, or at least its best
effort to do so. There are many problems with getting this exact and
I don't think the server does anything fancy to overcome them. When
Coot reads the file it calculates the rms deviation from 0.0 and
reports the contour level both relative to that rmsd and in raw units
(whatever they were, Coot could care less).
Some programs "normalize" the maps they calculate so the rmsd will
be equal to 1.0. When Coot reads such a map its two contour level
indicators will be the same.
If you load the same map into Pymol and ask it to normalize the
density values you should set your contour level to Coot's rmsd level.
If you don't normalize you should use Coot's e/A^3 level. It is
quite possible that they could differ by a factor of two.
Dale Tronrud
On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote:
> Hello. I am struggling with an old question--old because I've found
> several discussions and wiki bits on this topic, e.g. on the PyMOL
> mailing list
> (http://sourceforge.net/p/pymol/mailman/message/26496806/ and
> http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the
> suggestions about how to fix the problem are not working for me,
> and I cannot figure out why. Perhaps someone here can help:
>
> I'd like to display (for beauty's sake) a selection of a model with
> the map about this selection. I've fetched the model from the PDB,
> downloaded its 2mFo-DFc CCP4 map, loaded both the map and model
> into both PyMOL (student version) and Coot (0.8.2-pre EL (revision
> 5592)), and decided that I would use PyMOL to make the figure. I
> notice, though, that the map 'level' in PyMOL is not equivalent to
> the rmsd level in Coot, even when I set normalization off in PyMOL.
> I expected that a 1.0 rmsd level in Coot would look identical to a
> 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in
> Coot looks more like a 0.5 level in PyMOL. Does anyone have insight
> they could share about the difference between how Coot and PyMOL
> loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some
> other normalization factor in PyMOL that I should set? Or, perhaps
> there is a mailing list post out there that I've missed, to which
> you could point me. :-)
>
> Alternatively, does anyone have instructions on how to use Coot to
> do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of
> the 2Fo-Fc map, contoured at "1.0" about a 3-residue-long
> 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection,
> carve=2.0, and after hiding everything but the selection, I have a
> nice picture ... but with a map at a level I cannot interpret in
> PyMOL relative to Coot :-/
>
> Regards, Emily.
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