[phenixbb] rotamers

Phil Evans pre at mrc-lmb.cam.ac.uk
Thu Mar 24 08:04:12 PDT 2011

One catch with truncating side chains is that if you calculate electrostatic surfaces (for what they are worth) then you will probably lose some charges (I believe)

On 24 Mar 2011, at 14:54, Nathaniel Echols wrote:

> 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.
> -Nat
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list