[phenixbb] secondary structure restraints

Nathaniel Echols nechols at lbl.gov
Fri Apr 8 10:42:37 PDT 2011

On Fri, Apr 8, 2011 at 9:21 AM, Panne Daniel <panne at embl.fr> wrote:
> I am having problems with the secondary structure restraints in phenix.refine (1.6.4-486). I wrote a ss restraints file and use this as an input file. In the log file I can see that the file is read but the atom selections used by phenix.refine do not correspond to those set in the restraints file.

Okay, the problem is that you're specifying the restraints in the
"Input file" field of the secondary structure options dialog.  This is
probably my fault for not making the purpose of that parameter clearer
- it is actually intended only for PDB files (e.g. taking a structure
from the PDB and using its HELIX and SHEET records to restraint your
model), and doesn't get used very much.  If you add your parameters to
the main input list in the config tab of the GUI, they should be
processed correctly.  (Note: if you are very confident about your
annotations, you will probably want to turn off outlier filtering of
hydrogen bonds, which will guarantee that all restraints will be


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