Tim,
> do the absolute values matter? I tend to adjust the level (visually) > so that the map shows what I want to show. Usually the pictures show > some of the environment so that one can judge the map level by > comparison, rather than absolute numbers. The scale always seemed very > inexact and serve mostly as guidelines. > My objective is publication of a result, which means that I've already convinced myself that the maps support the interesting structural feature. Therefore, as guidelines, the maps in Coot were indeed helpful to me. But for publication, not only do I want to provide an intelligible, meaningful mage, but I want to describe the image in such a way as to make the view reproducible. I suppose that as long as I state which visualization program was used to make the image, and the settings involved, that should suffice for reproducibility's sake. But I've never seen anything in publications along the lines of the unitless "map level" used within a PyMOL session in which the map was generated and manipulated. Rather, the text always says that the map "was contoured at 3.5 sigma", or whatever is considered widely appropriate per the map used. I suspect that people assume that the map level in PyMOL is a sigma of some sort, but it was not clear to me (maybe still isn't ...) what standard deviation--if that is what it is--is actually calculated. Emily. > On 06/01/2015 11:32 PM, Paul Emsley wrote: > > On 29/05/15 21:15, 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 :-/ > >> > > > > Dear Emily, > > > > Sorry for the delay. > > > > 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. > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1 > > iD8DBQFVbVVWUxlJ7aRr7hoRAnbMAJ4kGS42VdXpllHLdnZjMIjCpwKmJQCg2DBP > ojupTPbXpTNXDhmAH4v+A64= > =293d > -----END PGP SIGNATURE----- >
