Hi Chris, - there is Phenix mailing list for Phenix-related questions. Please check http://www.phenix-online.org/
- the data resolution of 2.5A does not mean hydrogen atoms are not present in the crystal. There are methods to account for them. For details see (and references therein): "On contribution of hydrogen atoms to X-ray scattering" http://www.phenix-online.org/newsletter/ and around pages 41-42 here: http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf - if there are reasons for not using H atoms (such as crude initial model, for instance), you can always trivially remove them: phenix.reduce model_with_H.pdb -trim > model_no_H.pdb All the best, Pavel On Mon, May 7, 2012 at 6:07 AM, Christopher Browning < christopher.brown...@epfl.ch> wrote: > Hi, > > I've generally used PRODRG to create paramater files for any ligands I > add during refinement with CCP4 and/or PHENIX. I've been trying READYSET > from PHENIX as it greatly helps refining some metal ion positions. But > when I use READYSET, any ligand I add (in this case EDO or ethylene > glycol) gets modified to contain hydrogens. My resolution is 2.5, > definitely not high enough to resolve the hydrogens, so why are they > added. Should I just leave them there? I have the same problem with > another structure which has bizarre sugar molecules so they are not > standard COOT/CCP4/PHENIX small molecules. > > As a test, I removed the hydrogens added to the ligands and the refined > protein coordinates are way different than when the hydrogens are left > in? > > > Cheers, > > Chris > > > > -- > Dr. Christopher Browning > Post-Doctor to Prof. Petr Leiman > EPFL > BSP-416 > 1015 Lausanne > Switzerland > Tel: 0041 (0) 02 16 93 04 40 >
