Dear all,<br><br>I was using ready set to get my pdb ready. It automatically built the ligand cif file from scratch too. And the phenix.refine was fine with the files from ready set.<br><br>Then I tried another method in which I threw everything that phenix.refine needs, including pdb file, ligand cif file, ligand pdb file, mtz. And phenix.refine ran smoothly again.<br>

<br>But the refinement results were different between these two ways. The R fac is 1% different. I think ready set is only making the phenix.refine easier by generating ligand and building H, but if I do all the work of ready set and prepare the files for phenix.refine. Aren&#39;t they supposed to give the same results back? Can anyone help me here? Thanks a lot.<br>

-- <br>Ming<br><br>