[phenixbb] links in phenix

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jan 25 11:09:53 PST 2012


Christian

Thanks for the model file. I will answer you questions here and maybe
send some files separately.


> I have a pdb with a sugar chain as ligand. I used phenix ready set to get the
> links according to the link remarks in the pdb. However when I look into the
> edits file. All links are defined as geometry restraints and despite it is alpha
> 1-4 all bond restraints differ slightly in their length. Within the pdb file the
> definitions for the links were set to alpha1-4.

I am working on getting phenix.refine to automatically recognise sugar
links but at the moment LINK between sugars are not translated to
edits because of the limitations of the .edits format. More on your
solution later.

>  A Similar thing happend with a peptide link between 2 Aminoacids which have
> not a continously numbering because of a deletion, but it is a simple peptide
> bond.

This LINK is not converted because phenix.refine automatically links
peptides that are in order in the chain (numbering is ignored) and
within 3.0 angstrom. To check this run

phenix.refine model.pdb data.mtz --dry

and you will get a .geo file. You can check in here to ensure that the
link is made. I use a simple program

elbow.refine_geo_display model.geo "GLY 249" "GLU 253"

to see the restraints setup by refine.refine.
> I modified the .link.edits file accordingly  for the sugars like this
> ----------
> refinement.geometry_restraints.edits {
>  apply_cif_link  {
>    data_link = ALPHA1-4
>    atom_selection_1 = name  O4  and chain B and resname GLC and resseq    1
>    atom_selection_2 = name  C1  and chain B and resname GLC and resseq    2
>
>  }
> }

As Nat said this won't work. More on this later.

> ------------
> And applied a trans link for the peptide bond

No need. phenix.refine automatically links the trans peptide from the
geometry (not the LINK) and changes the ideal value for omega to 180.
Once again, the .geo file will confirm this.


>
> A second question is a very non standard peptide link due to a SNN residue in
> the chain. Based on the link a geometry restrain is created througn
> phenix.link_edits  There is a slight difference in the length between the N-
> terminal and the C-terminal peptide bond. Which is probably fine and the
> resoution is good enough (roughly 2 Ang.) that is looks fine, but no angle
> definitions for phi psi and so on are stated. What is the best way to define
> this two bonds correctly for the subsequent refinement?

You have touched on an interesting point. There are two ways to link
in this situation. The LINK record only defines a bond and angles
would be better. You can run an alpha script

elbow.ligand_linking model.pdb

to get two files. First the apply_link.def

refinement.pdb_interpretation.apply_cif_link {
  data_link = SNN-ASP
  residue_selection_1 = chain A and resname SNN and resseq  370
  residue_selection_2 = chain A and resname ASP and resseq  369
}

refinement.pdb_interpretation.apply_cif_link {
  data_link = GLY-SNN
  residue_selection_1 = chain A and resname GLY and resseq  371
  residue_selection_2 = chain A and resname SNN and resseq  370
}

specifies the residues to apply the links. Now the data_link.cif

#
data_link_GLY-SNN
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
GLY-SNN  1  CA       2  N1        coval       1.429689    0.020
#
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
GLY-SNN  2  N1       1  CA      1  C        109.471221    3.000
GLY-SNN  1  CA       2  N1      2  C5       109.471221    3.000
GLY-SNN  1  CA       2  N1      2  C2       109.471221    3.000
#
data_link_SNN-ASP
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
SNN-ASP  1  N3       2  C         coval       1.429689    0.020
#
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
SNN-ASP  2  C        1  N3      1  C3       109.471221    3.000
SNN-ASP  1  N3       2  C       2  CA       109.471221    3.000
SNN-ASP  1  N3       2  C       2  O        109.471221    3.000

specifies the bonds and angles. You should adjust the values as you
see fit because the bond length is taken from the geometry and the
angle is tetrahedral. You can also add torsions, plans and chirals.

Now about the sugars.  You can add

refinement.pdb_interpretation.apply_cif_link {
  data_link = ALPHA1-4
  atom_selection_1 = name  O4  and chain B and resname GLC and resseq    1
  atom_selection_2 = name  C1  and chain B and resname GLC and resseq    2
}

and check it in the .geo file. Hopefully, this will be redundant in a
few months.

>
> A third question is a alpha1-4 link which extend to a symmetry related sugar.
> How I incorporate the symmetry information into the link?

The symmetry operations are only available via the bond links in
.edits format. I can help you with that but if you put a sym op in the
link it is converted to an edits. Also COOT will tell you the sym op
as can a alpha script in PHENIX.

Cheers

Nigel

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


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