[phenixbb] rotamers

Nathaniel Echols nechols at lbl.gov
Thu Mar 24 07:54:12 PDT 2011

On Thu, Mar 24, 2011 at 2:41 AM, Antony Oliver
<antony.oliver at sussex.ac.uk> wrote:
> Although I can see from the non-crystallogapher end-user perspective that the zero occupancy option is probably preferred, because as at least the side-chain atoms are preserved, and readily identifiable when working in PyMOL, CCP4MG, Coot etc.

But if the naive end user sees an arginine sidechain sticking out,
he/she will most likely assume that the coordinates reflect reality.
I'm inclined to agree with Frank - we're not making theoretical models
here, so we shouldn't be guessing coordinate positions.  Even in a 4A
structure, however poor the sidechain density is, the coordinates have
been refined against the data, and the B-factors will still provide
some information about disorder and accuracy.  If end users demand
complete sidechains, let them make their own - this is far less
confusing (and less dangerous) than making something up and expecting
them to figure out what the zero column means.


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