What about the bogey of Fourier truncation ripples--I have heard many have been fooled by the into thinking they were seeing orbitals. How does one tell the difference?
JPK -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Phil Jeffrey Sent: Thursday, February 05, 2015 3:52 PM To: [email protected] Subject: Re: [ccp4bb] proton scattering by X-rays Mark, In the small-molecule crystal structures I work with it's relatively common to see localized difference electron density along covalent bonds or in the places you'd expect to see lone pairs during refinement after you've fit and modeled the atoms reasonably well and the phases are pretty good. It's usually not as strong as difference density for hydrogens, before you put them in, but it's often pretty clearly visible once you have. (I use SHELXLE as an interface for small molecule refinements because of a somewhat Coot-like experience in viewing maps). Phil Jeffrey Princeton > What you CAN do in fact is appropriately subtract "spherical electron > density" from the experimental density and see what is left (i.e. > directional ED that is 'surplus'). I tried to quickly find a paper on > that, they exist, and they show that experimental density does confirm > what we learn in chemistry class, orbitals are not imaginary. > > Mark
