[phenixbb] adding ligands to model

Geoffrey Feld gkfeld at berkeley.edu
Sun Feb 20 16:44:55 PST 2011


I have a few structures I am trying to refine that have density for ligands,
and I'm having trouble getting phenix to refine them properly. There are two
unique scenarios, so I'll go in order of difficulty.

1) There are non-water solvent molecules (i.e. probably PEGs) that are here
and there in the structure. I used phenix.elbow with SMILES notation to
build the requested ligands and placed / real space refined them into the
density using COOT. Now I cannot get phenix to refine the structure, every
time I get the message "Number of atoms with unknown nonbonded energy type
symbols: XX
    Please edit the PDB file to resolve the problems and/or supply a
    CIF file with matching restraint definitions, along with
    apply_cif_modification and apply_cif_link parameter definitions
    if necessary.
    Also note that phenix.ready_set and phenix.elbow are available
    for creating restraint definitions (CIF files).

where XX can be any variation of a number, depending on how I set up the
phenix.refine run. This is what I've tried:

a) adding the .cif files into my .def file I'm using for refinement
b) adding the .cif files on the command line
c) running phenix.ready_set to generate .cif files for the unknown ligands
and then inputing the .cif files from that on the command line
d) running phenix.elbow with --add_all and the pdb to generate .cif files
for unknown ligands, then doing as in (c) from the command line

None of these seem to get phenix.refine to skip the error mentioned above
and start refining. There are 3 different ligands, one of which is repeated
4x, but each has its own chain number in the same chain (I've even tried
them each with their own unique chain). Any advice on getting these ligand
restraints into phenix so it will happily refine?

2) I have an intramolecular crosslink in another structure, basically I
crosslinked two cysteines with 1,3-dichloroacetone, giving a
Cys-S-CH2C(=O)CH2-S-Cys linkage. How can I get restraints for this crosslink
so it will refine as one covalent chain? So far, I've placed the acetone in
between the two Cysteines, but it would be nice for it to be a part of the
chain so I can refine it in real space, the density is not so good since the
crosslink adds flexibility to the bond as apposed to just a disulfide. Any
ideas here? I thought maybe the best way to do it is to just modify one of
the cys to contain the extra atoms and call it a new residue, then add bond
restraints for the 2nd link, however, then I'm still stuck with the extra


Geoffrey K. Feld

Department of Chemistry
492 Stanley Hall
University of California, Berkeley

"Vigilia pretium libertatis"
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