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Thomas, > 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. > I posted the same question to the Coot mailing list (the thread can be found here: https://goo.gl/YjVtTu) , and got the following reply from Paul Emsley; I highlight the questions that I think you could best answer, with '***': "[ ...] I suspect that the issue is related to different answers to "the rmsd of what?" In Coot, we use all the grid points in the asymmetric unit - other programs make a selection of grid points around the protein (and therefore have less solvent). More solvent means lower rmsd. If one then contours in n-rmsd levels, then absolute level used in Coot will be lower - and thus seem to be noisier (perhaps). I suppose that if you want comparable levels from the same map/mtz file then you should use absolute levels, not rmsd. ***What does PyMOL's "1.0" mean in electrons/A^3?*** Regards, Paul." Regards, Emily. > On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) <[log in to unmask]> > 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----- > > > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > >