On Mon, May 25, 2015 at 2:35 AM, mohamed noor
was referring to the partial charge in the restraint file, which IMHO should be translated to the model.
The PDB file format is for formal integer charges. The partial charges will simply not fit.
I have a second problem - I'm using the cif file for refinement but the angles and bond lengths still get distorted. These are flagged as outliers in phenix.refine. Why is it not using the values that I input? My resolution is 3.8 A, but I still end up with positive density around all the hemes. In fact, the problems with hemes are the cause of a large majority of my outliers. I did a parallel refinement with and without the restraint file - it doesn't make any difference.
Please send the final model and .geo file directly off-list. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov