[phenixbb] rotamers

Ed Pozharski epozh001 at umaryland.edu
Mon Mar 28 10:04:53 PDT 2011


> - what you mean by "no density",

Lack of confidence in placement of the side chain.  Everyone would have
somewhat different take on it, but the question is more about what to
do, not how to decide if the side chain is disordered.

> Therefore this raises another item for your questionnaire: 

There is "other" option, feel free to use it

> refine group 
> occupancy for these atoms (one occupancy per all atoms in question - the 
> occupancy typically will refine to something less than 0.5 or so).

This raises an entirely different question regarding reliability of
occupancy refinement in general due to its correlation with the
B-factors.  Another can of worms.

> This trick with smearing out an atom by B-factor may only work for 
> isolated (single) atoms  such as waters because they are not bonded to 
> anything through restraints.

Certainly, presence of restraints makes the B-factor increase less
steep.  I just looked at an instance of a disordered arginine (no
density above 1 sigma for any side chain atoms), and B-factors jump from
30 at the backbone to 90 at the tip of the side chain.  This would
reduce the density level ~5x, which is probably quite sufficient for
blending it into the solvent.  There could be a bit of a problem in the
middle, where B-factors are inflated/deflated, but it does take care of
density reduction.

Things like atom-specific restraints and modified restraint target may
be of some help, but the effect on the final model may be too small to
validate the effort.

"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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