[phenixbb] MSE gap

Pavel Afonine PAfonine at lbl.gov
Wed Jan 16 13:51:25 PST 2008

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!

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
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