Tim is making a very good point (as usual!) The RMSD of the whole asymmetric unit is only a rough guide to a useful map contour - that depends on the relative B values of the feature you want to display. It is pretty obvious that features with lower than average B factors show up at higher Sig level than perfectly well defined features which have higher B values. One of the best COOT features is being able so easily to adjust the contour to something sensible .. Eleanor
On 3 June 2015 at 19:14, James Holton <jmhol...@lbl.gov> wrote: > I have never trusted Pymol's "normalization" of maps, because it has never > been clear to me if it does the normalization before or after the "carve". > If it is after, then you have a serious interpretation problem: the "1 > sigma" level will be MUCH lower than if the rest of the map were not set to > zero. In this situation if you set the "carve" right the map will look a > LOT more like the coordinates than it should. In fact, if you "normalize" a > map using anything but an integral number of asymmetric units your "1 > sigma" level will not be the same as if it were done properly. With pymol > you usually have to extend the map to "cover" the protein of interest, and > this extended map is seldom an integral number of asymmetric units. > > So, I have always taken to normalizing the map myself (using mapmask) with > a single ASU or single cell as the map extent, and THEN extending the map > to cover the PDB (using a completely different run of mapmask) and only > then load it into pymol. I always turn off map normalization in pymol. I > have also never used "carve", as my thesis adviser strongly disapproved of > the practice. Mostly because of the potential for bias mentioned above. > > Do you really have to "carve" for your density to be clear? > > -James Holton > MAD Scientist > > > > 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. >> >
