The validation of ligands performed by the PDB uses Mogul. If you have Mogul installed (free to most academic institutions, AFAIK), you can ask eLBOW to define the bonds and angles using Mogul thus providing geometry closer to the target. Discussions of whether this is a sound idea aside, you can avoid many of the validation issues. Metals are always tricky so for AD9 you may still be liaising with your annotator. I can send you a set of Mogul restraints for AD9 if desired.
Phenix and CCP4 ship with their own restraints libraries. You can point Phenix to the CCP4 libraries but you will remove some features from the Phenix tools. Either way, you can load a restraints dictionary that you have generated into Coot to do RSR etc.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov