Hi Dirk,
this is very interesting! From the list of changes, it appears that in
version 1.6.1, you use a similar idea to implement hydrogen bonds via
DSSP during refinement that I used to stabilize the 4.3 A refinement
of Pol II in complex with TFIIB [1]:
(...)
Could you please give more details of how this is implemented? What
are your hydrogen bond target distances and sigmas? Do you update this
list during refinement?
In phenix.refine documentation:
http://www.phenix-online.org/documentation/refinement.htm
look towards the bottom of the page for "secondary_structure". All the
parameters are defined there. If you still have any questions, please
let Nat or me know (Nat added this option so he may provide with more
details).
The documentation for secondary structure restraints is still missing,
sorry. Hopefully Nat adds it soon.
Pavel.
