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
On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
Dear PHENIX users,
I wonder what is the 'correct' way of (re)defining geometric restraints among atoms.
Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners?
Thank you in advance for your help!
-- 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