[phenixbb] cif links for ligands bound to atoms in alternative conformation.

Pavel Afonine PAfonine at lbl.gov
Mon Jul 20 21:47:10 PDT 2009

Hi Maia,

I might be misunderstanding your question, but can't you define the bond 
between these atoms using "custom bonds":



You can select such atom like this:

"chain X and resseq 123 and name YZ and altloc A"

You can experiment with atoms selections (to see which exactly atoms you 
are selecting) using this very handy tool:

phenix.pdb_atom_selection model.pdb "your_atom_selection_string"


On 7/20/09 5:21 PM, Maia Cherney wrote:
> Hi all,
> I need to make a cif_link_params file for a covalent ligand bound to a 
> sulfur in one of the alterantive conformations. What is the syntax for 
> such an atom: SG_A or ASG or A_SG etc?
> Maia

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