On Fri, Apr 8, 2011 at 9:21 AM, Panne Daniel 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.

Could you please send me (off-list) the file containing the SS restraints, and the log file from your run? I suspect there is a syntax problem, but it's hard to guess without seeing the output. FYI, I've fixed a lot of bugs in this code recently, so I'd recommend upgrading to the latest nightly build. -Nat

On Fri, Apr 8, 2011 at 9:21 AM, Panne Daniel 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 generated.) -Nat