Hi Mike, if you send me the inputs (data, model and any parameter files) I will tell you what's wrong. If you choose to send the files, please do so to my email address (not the whole mailing list).
FYI: there is Phenix mailing list for questions like this. Pavel On Tue, Mar 5, 2013 at 10:11 PM, Mike John <[email protected]> wrote: > Hi, Everybody, > > For refinement of ion in my structure, I used phenix.metal_coordination to > produce a geometry restraints file elbow.edits. But after including the > file in the phenix refinement, the refined pdb has clash between metal and > one of the coordinated atoms, as shown in the attachment. I double checked > elbow.edits file, the bond restraint between the two clashed atoms is > clearly in the file and included in the refinement. Is this a bug in phenix > or I did something wrong? > > Thanks! > > >
