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> > This a side effect of the idiocy of setting a contour level as a multiple > of the so-called "sigma" level (a battle that some of us have fought & lost for many years). This is actually the RMS deviation over the volume of the map box, so if this includes a larger volume of solvent the RMS value will be smaller, ie it is a funciton of the box size!. Maps from refinement programs (when there is a model) are on an absolute scale in e/A^3 and it makes sense to set contour levels in these units, which are independent of the box size. > It seems like I was causing my own problem...I rotating a full-cell Fc map with a single molecule, and comparing with a full-cell Fc map with both molecules (in order to verify that I'd translated the PHASES NCS operator (polar coordinates) into relevant CCP4 operator). As soon as I tried it with the experimental maps (also full-cell), the sigma/rmsd values started behaving as expected. However, the discussion of using rmsd for a contour cutoff reminded me of a (probably bad) idea I'd had a while back. Why use contour surfaces at all, instead of color-mapping the value of the map at a given point? This would probably result in a higher load on the graphics card, and some care with transparency, but seems like it would give a better visualiation of the map (at least with stereo; in 2d this might be even more confusing). Any ideas if this has been tried before (or reasons why it's a bad idea)? Pete Pete Meyer Fu Lab BMCB grad student Cornell University
