Hi Troy, one way of going doing this is (if atoms are not too far away, although try anyway) (Ralf may have a better idea): 1) Use custom bonds between these two atoms N and C for a short and simple refinement run just to close the gap. To do this, create a file "custom_bond.param" and put the following lines there: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = "chain A and resid 125 and name C" atom_selection_2 = "chain A and resid 125 and name N" distance_ideal = 1.4 sigma = 0.02 } } and run phenix.refine like this: % phenix.refine model.pdb data.mtz custom_bond.param In this context the precise value in "distance_ideal = 1.4" is not important: all you want at this step is to bring these two atoms close enough so next time you run phenix.refine it automatically recognizes the covalent bond. Hopefully this refinement run will bring these two atoms close enough. 2) After the gap is closed in "step 1)", run all your subsequent refinement jobs without specifying the file "custom_bond.param", so the proper value for "distance_ideal" is used (and angle as well). Please let us know if this didn't help or you have any questions! Pavel. On 1/16/2008 1:31 PM, Troy E Messick wrote:
Hello,
I seem to be having a problem with phenix.refine and the seleno-methionine residue (resname MSE).
It seems that I have a gap in the peptide bond between the C atoms and the N atom of the subsequent residue. Is there something I could add to the restraints_edits.params file to get it to click together? What is the distance_ideal and sigma for a peptide bond?
Thanks for your help, Troy _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb