[phenixbb] links in phenix

[Nigel Moriarty]

Christian

Can you send me the file (directly), so I can look in detail at each question.

Nigel

> 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.
>  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.
> 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
>
> I added the modified file as additional parameter file in the gui. However in the
> final .eff file I found just the old restraints from the previous run. In the
> final .eff file it is stated that the file with my updated links is loaded
> ------
> gui {
>    base_output_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix"
>    tmp_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix/phenix/tmp"
>    send_notification = False
>    notify_email = "christian.roth at bbz.uni-leipzig.de"
>    add_hydrogens = True
>    skip_rsr = False
>    phil_file =
> "/homes/roth/structure/250/082_c2_5/refinement/phenix/refmac20link.link.edits"
> -----
> 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?
>
> 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?
>
> A third question is a alpha1-4 link which extend to a symmetry related sugar.
> How I incorporate the symmetry information into the link?
>
>
> 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
>
> I am sorry for this long Mail and so many question. I hope you could help me
> to clarify some the things.
>
> Best Regards
>
> Christian
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-- 
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