[phenixbb] links in phenix summary

David Shin davidsshin at lbl.gov
Wed Apr 3 20:11:21 PDT 2013

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
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.



On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth <
christian.roth at 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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> phenixbb at phenix-online.org
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David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
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