Robert Hanson wrote: > Keep talking, Rich. I don't quite have it. > > I have a file of numbers. An isosurface is produced not by contouring > but by finding the surface that intersects that cube of numbers at a > specific "cutoff" value. > > > dmin dmax dmean (density min max mean) > > > > rms > > > >1 sigma = 1 esd = 1 rmsd*rmsd > > > esd is what? Sorry, I really need this from the beginning. Is that the > value I read from the file? > > What I'd like to know is what the "rms" in the file is referring to: > > FileManager opening 3hyd_map.ccp4 > MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891 > MRC header: rms: 0.74718976 > > Is that really the square root of the average of the squares of the > numbers? I guess it could be.... The rmsd isn't calculated from the dmin/dmax values but comes from a separate calculation which generates the map itself.
When calculating the electron density value an associated calculation determines the likely error in that value and that error is the estimated standard deviation (errors are assumed to be distributed following a normal distribution curve). The rmsd value is simply the square root of the esd value. So for a point in the cell the calculation of the electron density might be, say, 3 electrons per cubic angstrom. To a crystallographer this number means more if the error associated with it is also known. So an additional calculation is run which will give a best guess for the error in those map values. Say that is 0.78 electrons. Thus for any value of the electron density we have an estimated error (standard deviation) of plus or minus 0.78 electrons. For the example you site above: the max. electron density in the map volume is 4.9988 e/A^3 with an rmsd of 0.747. Or to express it as an esd (i.e. sigma): 5.0 e/A^3 +/- 0.6 (the square of 0.747). Similarly, the minimum density is -1.2 e/A^3 +/- 0.6. I'm not sure how you want to generate the isosurface but if you are just giving it a single cutoff value then use 0.6 as a 1 sigma cutoff isosurface or 1.2 for a two sigma cutoff isosurface, etc. Rich ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
