[phenixbb] rotamers

Kendall Nettles knettles at scripps.edu
Tue Mar 29 18:43:03 PDT 2011

We have been doing a lot of parallel refinements where we are checking out the new options in PHENIX refinement, and one of the things we have observed is that sometimes the sidechains with no clear electron density end up in the main chain density, and distort the model. There is no clear pattern as to which options lead to this phenotype, as different combinations give different results. Until we can sort out what is causing this, it seems clear to me that it is better to delete the side chains. If you want to leave a side chain with no clear electron density, you have to make sure each one is not distorting the model. So leaving the side chains with no clear electron density requires much work, with a benefit that is not clear to me. 

Kendall Nettles

On Mar 28, 2011, at 1:04 PM, Ed Pozharski wrote:

> Pavel,
>> - 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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