[phenixbb] adding ligands to model

[Nigel Moriarty]

Geoffrey


> 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.

Run

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.

http://www.phenix-online.org/documentation/refinement.htm#anch84

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

Nigel

-- 
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