Thanks Paul. To help with others' future Googling efforts on the topic of PyMOL versus Coot map levels, I'll leave here the link to the discussion that began from my initial post, on the ccp4bb: https://www.mail-archive.com/[email protected]/msg39219.html
> >> >> Alternatively, does anyone have instructions on how to use Coot to do >> what I'm trying to do in PyMOL? > > Is there a way in Coot to display a selection of the map about a set of residues - something akin to PyMOL's 'carve' option? > 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). This makes sense to me - thanks for the clear response :-) It appeared to me--and it turns out to be pointless, IMO, to supply an image to prove my point, because the image is too crowded--that the Coot map was much tidier/less 'noisy' around my selection of residues. In fact, I wondered if Coot was sampling the map more/at higher frequency (?) than is PyMOL. I'll have to Google more about that; there are probably settings I need to adjust. Anyway, it definitely didn't seem noisier than PyMOL's display of the same map, which is why I am asking if Coot has something like a 'carve' feature. > 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? > I don't know how PyMOL's map level relates to electron density, but in case Thomas Holder knows, I'll ask the question at the related ccp4bb thread where he's participating. I guess you're asking about how the maps are scaled in PyMOL? ...how are they scaled in Coot? The idea of an absolute scale, frankly, confuses me, so I am fine to take the last two questions back to my crystallography notes :-) Thanks, Emily. > Regards, > > Paul. >
