[phenixbb] adding ligands to model

Nigel Moriarty nwmoriarty at lbl.gov
Mon Feb 21 08:44:03 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).

This is because when you use only the SMILES string, eLBOW makes up
the atom names and they don't make whats in the model.

> phenix.refine run. This is what I've tried:
> a) adding the .cif files into my .def file I'm using for refinement
> parameters
> 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

This should have worked unless you have a very unusual PDB file. Can
you send me the PDB?

> 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
> hydrogen.

I would recommend the following.

Generate a restraints file for the linking molecule.

Put it in place.


elbow.ligand_linking model.pdb

This is an alpha release program that will attempt to generate the
links for you. If that fails you can create your own by reading this.


I'm also happy to take a look at your model file.


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

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