Hi Maia, I assume that these waters are already present in your structure. Then run phenix.phenix.metal_coordination model.pdb That will create a restraints file for you Mg2+. Edit it, if necessary, to satisfy your expectations. These two waters should be there. Run phenix.refine and give it that restraints file. If you run phenix.refine with "ordered_solvent=true" option, then phenix.refine may or may not remove these two waters. If you absolutely need to keep these waters, run phenix.refine with "ordered_solvent=true" untill the last moment, then add two waters and run it again with "ordered_solvent=false". Something like this... Pavel. On 3/27/10 3:50 PM, Maia Cherney wrote:
Hi Pavel,
I have 2 important waters at 2.12 A distance after refinement. They are ligands of Mg2+. How can I restrain this distance to 2.3A (to pass pdb validation)? Is it in the ordered solvent that I need to change the default h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2
Maia
Pavel Afonine wrote:
Hi,
phenix.refine removes F-obs outliers for refinement. See .log file for the number of such reflections. Also, it automatically removes Fobs=0. Do phenix.mtz.dump data.mtz to see the content of your MTZ file.
Pavel.
On 3/27/10 1:26 PM, r n wrote:
Hi all I observed that for the same data set and resolution, number of reflections for the refinement is different values both in phenix (9488), refmac5 (9423) and refmac using coot interface (9530).
Please anyone can let me know why the differences between the programs for same resolution and data.
Thanks ram
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