[phenixbb] EG4 not in phenix dictionary?
pafonine at lbl.gov
Mon Jun 3 14:35:07 PDT 2013
(***Nigel would normally reply to this but he is away for vacation, so
I'll try to reply***)
phenix.refine uses a subset of CCP4 monomer Library with useless entries
removed ("useless entries" = those that are missing information
mandatory to run refinement).
In Chemical Components library EG2 stands for
If that's what you want then getting PDB and CIF files is a matter of
running this command:
If this is not what you want, then find the correct 3-letter code for
your ligand and run the above command using it.
Also, you can use a smiles string, example:
"Nc1ncnc2[n](cnc12)[C@@H]3O[C at H](CO[P@](O)(=O)O[P@@](O)(=O)OP(O)(O)=O)[C@@H](O)[C at H]3O"
Alternatively, you can just take your PDB file with the ligand and run
which will create CIF files for all unknown to Phenix ligands in it.
However, it is still a good idea to make sure that you name your ligand
On 6/3/13 2:16 PM, Yarrow Madrona wrote:
> I have previously refined EG4 and EG2 (tetra and diethylene glycol) as
> ligands and these were in the standard phenix library. I was under the
> impression that phenix shares the library from the CCP4 monomer library
> which I know should have EG4.
> Can anyone help me with this. I guess the alternative is to generate a
> restraints file.
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