sorry to bother! ...of course it was silly : the 'shared' Zn atoms are on special positions, so I guess the best way to go is to refine their positions with 0.5 occupancy and that's it (the bond distance with the symmetric of course already being taken into account on the ASU's contents!) best alejandro Alejandro Buschiazzo wrote:
Thank you Nigel!
I'll try this immediately.
...in the meantime, I still have a question for you : will this handle as well the coordination with atoms on symmetry-related protein neighbors? (don't see those in the elbow.edits that phenix.metal_coordination generates...or am I missing something silly here?)
ale
Nigel W Moriarty wrote:
Alejandro
There are a number of options. The most direct is to use
phenix.metal_coordination --use-default-bondlengths=1 model.pdb
to get an "edits" file which contains a number of bond and angle directives for phenix.refine. Without the --use-default-bondlengths option, the bonds in the model.pdb are used as ideal distances. With the option, the ideal values are quantum chemical calculated distances.
Always look in the edits file to make sure it contains the restraints you want. You can remove some (angles are the most likely candidates) and add if desired.
You can also run
phenix.ready_set model.pdb
which will generate the "edits" file and add hydrogens to your model.
Nigel
-- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185