On Wed, Jan 25, 2012 at 2:31 AM, Christian Roth wrote:

Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening?

Yes, and I'll fix that ASAP today... (sigh)

A last question regarding the hydrogens in refinement. For rebuilding it is nice to remove the hydrogens. Normally I use the commandline for this purpose. But It would be nice to do it automatically after refinement as a third pdb output in addition to the two standard outputs phenix_output.pdb and the phenix_output_reduce.pdb. Is there an option in the GUI to do this automatically. I thought I have seen this previously but cannot find it anymore

You're not the first person to ask for this, but I think we decided that we wanted to discourage people from depositing PDB files that had been modified post-refinement. However, since the PDB annotators often (usually? always?) do this anyway, we may be waging a futile battle. -Nat

On Wed, Jan 25, 2012 at 2:31 AM, Christian Roth wrote:

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

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

Okay, looking at this more closely, I think the parameter scope is wrong - it should be: refinement.pdb_interpretation { apply_cif_link { ... } } This would explain why it isn't working - the parameters are being discarded because they're not recognized. Details here: http://www.phenix-online.org/version_docs/dev-968/refinement.htm#anch88

Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening?

Just to double-check, could you please send me (off-list) the .eff file for the run? I suspect I know what is going on - probably an inconsistency in GUI behavior, which I recently changed because the old way was just broken. -Nat

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 : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov