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You are correct about this. The magnitude of this effect depends on the amount of solvent in your crystal (which tends to be flatter) but it rarely reaches a factor of two. This does point out a serious flaw with contouring a map relative to its rms (one of many). If you calculate a map that just covers the "interesting" part, it probably contains a lot of features. The rms calculated from that region of the map alone will be larger and your features will look smaller. If you set a contour level relative to e/A^3 the appearance of the image will not depend on the region of space covered by your map nor the percentage of solvent in the crystal. Dale Tronrud On 6/1/2015 9:16 AM, Thomas Holder wrote: > Hi Emilia et al., > > I tried to figure out the PyMOL vs. Coot normalization discrepancy > a while ago. As far as I remember, PyMOL normalizes on the raw data > array, while Coot normalizes across the unit cell. So if the data > doesn't exactly cover the cell, the results might be different. > > Cheers, Thomas > > On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) > <ec...@drexel.edu> wrote: >> 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. >> >> This is what I was looking for! (i.e. what the units are) Thanks. >> :-) Yes, I'd downloaded the 2mFo-DFc map from the EDS, and got >> the same Coot v. PyMOL discrepancy whether or not I turned off >> the PyMOL map normalization feature. >> >> 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. >> >> This was exactly the case. The map e/A^3 level (not the rmsd >> level) in Coot matched very well, visually, the map 'level' in >> PyMOL; they were roughly off by a factor of 2. >> >> I did end up also generating a 2mFo-DFc map using phenix, which >> fetched the structure factors of the model in which I was >> interested. The result was the same (i.e. PyMOL 'level' = Coot >> e/A^3 level ~ = 1/2 Coot's rmsd level) whether I used the CCP4 >> map downloaded from the EDS, or generated from the structure >> factors with phenix. >> >> Thanks All. >> >> Emily. >> >> >> >> 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. >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) >> >> iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ >> nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -----END PGP >> SIGNATURE----- >> > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVskp8ACgkQU5C0gGfAG12urQCfQs1pkluJuYXVtULqNrBcBLE8 vykAoJ8fOqU2BnmGmNj+qspFX4/7Jo4T =LMS8 -----END PGP SIGNATURE-----
