[phenixbb] links in phenix

Christian Roth christian.roth at bbz.uni-leipzig.de
Wed Jan 25 02:31:35 PST 2012


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 
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 = 
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


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