[phenixbb] MSE gap

[Troy E Messick]

Thanks, Pavel, for your suggestions.

As far as I can tell, there isn't a gap in the input pdb file, and
phenix.refine is creating the gap.  I was thinking of using the
refinement.geometry_restraints.edits to define the distance and angle,
however, I wasn't sure what the distance_ideal and sigma is for a
peptide bond.  I think without specifying the restraints,
phenix.refine will keep creating the gap, so I think your idea about
doing a final round of refinement without the restraints will work.

Troy

On Jan 16, 2008 4:51 PM, Pavel Afonine <PAfonine at lbl.gov> wrote:
> 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
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>