[phenixbb] Real space refine of long side chains

Pavel Afonine pafonine at lbl.gov
Tue Nov 26 11:02:16 PST 2019


does anyone has a clear example that demonstrates this issue and that 
you can share with me? Having such an example would be most helpful as 
it will allow me to investigate the problem and hopefully address it 

I suspect this can potentially happen at low resolution (perhaps 4-4.5A 
and lower) when main-chain density looks like tubes and there isn't much 
density for side chains, so the main chain density attracts side chains. 
However, with default setting this should not happen as there are 
rotamer restraints. So I'm still not sure what's happening and this is 
why I'm looking for an example.


On 11/26/19 03:55, Leonid Sazanov wrote:
> Hi,
> We have addressed exactly this problem by writing a script, in which 
> B-factors are refined first and only then real-space refinement happens.
> This allows disordered side-chains to acquire high B-factors and so 
> they are not pulled into backbone anymore.
> This cycle is repeated twice to achieve convergence.
> Parameters for B-factor refinement (ADP restrains) were optimized to 
> account for consistent lack of density for acidic side chains in cryoEM.
> It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
> If needed, I can send a script.
> Best
> Leonid

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