Hi, 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 centrally. 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. Thanks, Pavel 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