[phenixbb] links in phenix

Nathaniel Echols nechols at lbl.gov
Wed Jan 25 09:26:21 PST 2012

On Wed, Jan 25, 2012 at 2:31 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> wrote:
> I modified the .link.edits file accordingly  for the sugars like this
> ----------
> refinement.geometry_restraints.edits {
>  apply_cif_link  {
>    data_link = ALPHA1-4
>    atom_selection_1 = name  O4  and chain B and resname GLC and resseq    1
>    atom_selection_2 = name  C1  and chain B and resname GLC and resseq    2
>  }
> }
> ------------
> And applied a trans link for the peptide bond

Okay, looking at this more closely, I think the parameter scope is
wrong - it should be:

refinement.pdb_interpretation {
  apply_cif_link {

This would explain why it isn't working - the parameters are being
discarded because they're not recognized.  Details here:


> Somehow the old restraits are already in the .eff file and the new ones are
> ignored how I could I avoid this. Simply closing the GUI an reopening?

Just to double-check, could you please send me (off-list) the .eff
file for the run?  I suspect I know what is going on - probably an
inconsistency in GUI behavior, which I recently changed because the
old way was just broken.


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