Hi -

I was trying to resolve some issues where I have an acetyl group at the N-terminus. Historically it appears, these are treated as a residue (say "ACE 0"). To provide phenix.refine with angles and bonds, I made a file similar to a metal.edits file:

One example of an angle between the acetyl and the first amino acid in my file:
refinement.geometry_restraints.edits {
  angle {
    action = *add
    atom_selection_1 = name C   and chain A and resname ACE and resseq   0
    atom_selection_2 = name N   and chain A and resname ALA and resseq   1
    atom_selection_3 = name CA  and chain A and resname ALA and resseq   1
    angle_ideal = 121.6367
    sigma = 5
  }
}

The problem I'm having is defining a plane such that what would appear to be a peptide bond is flat: ACE O - ACE C - ALA N - ALA H
I'm just not sure if it's being taken care of, there is a slight bend after refinement, but this also matches the electron density somewhat.

I tried to run elbow.ligand_linking , but appears to be missing from the release I have:  phenix-1.8.2-1309

Anything help appreciated.

Thanks,

Dave

On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth <christian.roth@bbz.uni-leipzig.de> wrote:
Dear all,

thanks to the phenix team which helped me a lot to resolve all issues
regarding the correct link definitions.

I have summarised a few things which one might consider if nonstandard links
are necessary.

Try phenix ready set to get your links out of the pdb. Do not forget to change
the possible LINKR to LINK!
Inspect the links and decide if they are useful!
Peptide links are automatically incorporated if residues are close (inspect
geo file)
Non standard peptide links could be created using using an now available alpha
release script:

elbow.ligand_linking model.pdb

Inspect the generated cif file and correct angles and incorporate dihedrals and
so on if necessary.

Sugar links which exists in the mon_lib.cif should be incorporated using the
apply_cif link option like
refinement.pdb_interpretation.apply_cif_link {
     data_link = ALPHA1-4
     residue_selection_1 = chain B and resname GLC and resseq    1
     residue_selection_2 = chain B and resname GLC and resseq    2
}
According to the link definition the C1 oxygen of the following sugar with the
higher number must be removed.
The automatic incorporation of sugar links will be probably soon available in
phenix. Nigel is already working on this.
If one want use hydrogens in the refinement, they have to be added previously
with ready_set and afterwards the OH4 sugar hydrogen has to be removed before
the refinement.

For links with symmetry related atoms the symmetry operator must be included
in a custom bond definition
efinement.geometry_restraints.edits {
  bond {
    action = *add delete change
    atom_selection_1 = chain A and resname HEM and resid 154 and name FE
    atom_selection_2 = chain A and resname MTO and resid 155 and name O
    symmetry_operation = -x,y,-z
    distance_ideal = 2.2
    sigma = 0.01
  }
}
The operator can be obtained using

iotbx.show_distances your.pdb > all_distances

Search for keyword "sym"
or from Coot clicking on the symm option. Coot print out the operator and the
translation term separately. Both has to be merged in the  final operator used
in phenix!

Christian
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David Shin, Ph.D
Lawrence Berkeley National Labs
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