Re: [phenixbb] geometry in phenix.refine

Is it possible that phenix.pdbtools ignored the H atoms when calculating the geometry statistics?

Currently no. But you can easily do it in two steps: 1) phenix.pdbtools model.pdb remove="element H" output.file_name=model_noH.pdb 2) phenix.pdbtools model_noH.pdb --show-geometry-statistics Pavel.