[phenixbb] Problem with LLP ligand

[Nigel W Moriarty]

James

Unfortunately, the Monomer Library uses the old (v2) hydrogen names 
(HE1, HE2) and your file is using the new v3 names (HE2, HE3).  It does 
seem that you are using the old names for some of the other atoms.  v2 
C5* compared to v3 C5'.

You can use ReadySet!

phenix.ready_set model.pdb

to help with the preparing for a refinement.

Regarding linking, because this is a non-standard aminoacid its a 
special case.  phenix.refine will recognize it and automatically link 
the main chain.  The link the Folmer sent would be useful in the case 
that you were using the residues LYS and PLP instead of the composite LLP.

If you have any more trouble contact me directly.

Nigel

On 8/19/09 2:02 AM, James Naismith wrote:
> 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
>
>
> -------------------------------------------------------------------------------
> Major third-party components of Phenix include:
>      Python, wxwidgets, wxPython, Boost, SCons, Clipper,
>      CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
>    Enter phenix.acknowledgments for details.
> -------------------------------------------------------------------------------
>
> 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
>
>
>
> The University of St Andrews is a charity registered in Scotland : No  
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>
>
>
>
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov