[phenixbb] MSE gap
PAfonine at lbl.gov
Wed Jan 16 13:51:25 PST 2008
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:
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:
> 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,
> phenixbb mailing list
> phenixbb at phenix-online.org
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