[phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.

Joseph Brock joeylives2ride at hotmail.com
Tue Jul 13 03:46:49 PDT 2010

Hi Ralf and Pavel,

Thanks so much for the quick response and advice.

I have tried both of your suggestions: To assign different altloc identifiers, with the same res ID, chain ID and different resnames (Ralf) and with the same resname (Pavel). I had thought of this but was afraid it would cause confusion with the associated .cif files. Unfortunately, this appears to be the case. 

For your strategy Ralf, the .cif and .pdb files created by "phenix.ready_set modified.pdb"


the .cif file created by "phenix.elbow modified.pdb" were all accepted by phenix.refine, however the two molecules were still driven away from each other =(

For your strategy Pavel, I could not get phenix.refine to run with either the pehnix.ready_set, or the phenix.elbow outputs. It consistently gives the following .cif file error:

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown nonbonded energy type symbols: 52
    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).

I will send to you the appropriate sections of both modified pdb files off list and the associated .cif files.

Thanks so much again to both of you for all of your help.



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