[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:
http://www.phenix-online.org/version_docs/dev-968/refinement.htm#anch88
> 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.
-Nat
More information about the phenixbb
mailing list