[phenixbb] Problem with LLP ligand

James Naismith naismith at st-andrews.ac.uk
Wed Aug 19 02:02:24 PDT 2009


Dear All,
			I am trying to refine a structure which has a Lys linked to PLP. In  
the PDB this is called  LLP.
When I take it through refine it crashes complaining about the ligand.

"Sorry : Fatal problems interpreting PDB file:
   Number of atoms with unknown nonbonded energy type symbols: 8
   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 (see phenix.refine documentation).
   Also note that phenix.elbow is available to create restraint
   definitions for unknown ligands.
Traceback:
None
"

I know I have to use REEL to fix this in some way. I have used REEL to  
make ligands not bound to protein before. It is how to do this when  
the ligand is covalently bound that I am stuck with.
Any help (particularly a cif restraints file!) gratefully received.



best
Jim


-------------------------------------------------------------------------------
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     CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
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-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Working crystal symmetry after inspecting all inputs:
   Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90)
   Space group: P 1 21 1 (No. 4)

   Monomer Library directory:
     "/usr/local/phenix-1.4-115/chem_data/mon_lib"
   Total number of atoms: 13558
   Number of models: 1
   Model: ""
     Number of chains: 3
     Chain: "A"
       Number of atoms: 6752
       Number of conformers: 2
       Conformer: "B"
         Number of residues, atoms: 420, 6747
           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':  
1, 'LLP,HE3': 1}
           Classifications: {'peptide': 420}
           Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
           Chain breaks: 3
       Conformer: "A"
         Number of residues, atoms: 420, 6747
           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':  
1, 'LLP,HE3': 1}
           Classifications: {'peptide': 420}
           Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
           Chain breaks: 3
           bond proxies already assigned to first conformer: 6820
     Chain: "B"
       Number of atoms: 6800
       Number of conformers: 1
       Conformer: ""
         Number of residues, atoms: 423, 6800
           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':  
1, 'LLP,HE3': 1}
           Classifications: {'peptide': 423}
           Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4}
           Chain breaks: 3
     Chain: "M"
       Number of atoms: 6
       Number of conformers: 1
       Conformer: ""
         Number of residues, atoms: 6, 6
           Unusual residues: {' SM': 6}
           Classifications: {'undetermined': 6}
           Link IDs: {None: 5}
   Number of atoms with unknown nonbonded energy type symbols: 8
     "ATOM   3149  HG3 LLP A 211 .*.     H  "
     "ATOM   3151  HE3 LLP A 211 .*.     H  "
     "ATOM   3153  HD3 LLP A 211 .*.     H  "
     "ATOM   3155  HB3 LLP A 211 .*.     H  "
     "ATOM   9896  HG3 LLP B 211 .*.     H  "
     "ATOM   9898  HE3 LLP B 211 .*.     H  "
     "ATOM   9900  HD3 LLP B 211 .*.     H  "
     "ATOM   9902  HB3 LLP B 211 .*.     H  "
   Time building chain proxies: 9.24, per 1000 atoms: 0.68



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