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Hi Yarrow, (***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 AMINODI(ETHYLOXY)ETHYLAMINOCARBONYLBENZENESULFONAMIDE If that's what you want then getting PDB and CIF files is a matter of running this command: phenix.elbow --chemical-component=EG2 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: phenix.elbow --smiles "Nc1ncnc2[n](cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]3O" Alternatively, you can just take your PDB file with the ligand and run ReadySet: phenix.ready_set model.pdb 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 correctly. Pavel On 6/3/13 2:16 PM, Yarrow Madrona wrote:
Hello,
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.
-Yarrow