> > > > 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----- >
