Alejandro Currently you have to have LINK records in your model.pdb that contain the symmetry details and use phenix.link_edits to generate the correct "edits". I'll have to look into putting the smarts into the metal_coordinate code. Nigel On 2/3/09 9:26 AM, 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
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!
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov