[phenixbb] Exploded ligands and phenix...

junfeng liu jliu at nimr.mrc.ac.uk
Tue Apr 28 06:23:10 PDT 2009


Hi Ruben,
This is always happened to build ligand into the poor electron density  
when the SA is on during refinement.
I always add ligand in the last refinement cycle without SA. That does 
work for me.
Good luck!
leo
Ruben Van der Meeren wrote:
> Hi,
>
> I'm using phenix for the refinement of my protein (phenix.refine). But  
> there is a problem...
>
> My protein contains a ligand. For this ligand I use the optimal  
> coordinates wich I downloaded from the HIC-Up server. Then, as coot  
> and phenix need a cif file, I generate a cif file using the PRODRG  
> Server and select (copy-paste) the Refmac5 output --> *.cif . Below  
> you can see the content of this cif file and also the pdb file.
>
> Coot can use this cif file. But when I refine the protein (e.g. even  
> only individual sites) the ligand "explodes". In coot you then see  
> only single atoms and no bonds. To illustrate this you can see a  
> pictures on this website:   
> http://gallery.me.com/ruben.vandermeeren#100216   --> "exploded"
>
> First I thought that phenix could not find the cif file, but the  
> correct path (via monomers) is given in the parameter file and I also  
> used the command line to import the cif file, but still the ligand  
> "explodes". I use the latest version of phenix for mac (phenix-1.4-3).
> But more important: I also tried refmac (from ccp4) to refined my  
> protein with it and here there is "no explosion". So refmac does  
> something that phenix doens't: it can refine my protein with the  
> ligand. You can see the nice picture on this website:  
> http://gallery.me.com/ruben.vandermeeren#100216   --> "as it should be".
>
> So my question is on how to resolve the issue using phenix.refine. Is  
> phenix somehow unable to read the contents of the cif file?
>
>
> Best regards,
> Ruben
>
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------
> PDB
>
>
> COMPND TRE TREHALOSE; ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE
> REMARK TRE Part of HIC-Up: http://xray.bmc.uu.se/hicup
> REMARK TRE Extracted from PDB file pdb1j1m.ent
> REMARK TRE Formula C12 H22 O11
> REMARK TRE Nr of non-hydrogen atoms  23
> REMARK TRE Eigen-values covariance X/Y/Z      187.8      54.6      26.5
> REMARK TRE Residue type TRE
> REMARK TRE Residue name   7347
> REMARK TRE Original residue name (for O) $304
> REMARK TRE  RESOLUTION. 1.50 ANGSTROMS.
> REMARK TRE occurs in       21 other PDB entries
> REMARK TRE Also in <1.5A     :  2BHY 2BY2 2BY3 2Z3G
> REMARK TRE Resolution (A)    :  1.50 1.50 1.50 1.50
> REMARK TRE Also in 1.5-2.0A  :  2BY0 2BY1 2BXY 2BXZ 1EU8 1F0P 2EBF 2CY6 2E4P
> REMARK TRE Resolution (A)    :  1.55 1.55 1.75 1.75 1.90 1.90 1.90 2.00 2.00
> REMARK TRE Also in 2.0-2.5A  :  2DXY 2FPD 1NI6 2B1Q 1V6A 2E50 2EBH
> REMARK TRE Resolution (A)    :  2.03 2.05 2.10 2.20 2.30 2.30 2.40
> REMARK TRE Also in 2.5-3.0A  :  1TEX
> REMARK TRE Resolution (A)    :  2.60
> REMARK TRE
> HETATM    1  C1  TRE  7347       1.108   0.876   0.900  1.00 20.00
> HETATM    2  C2  TRE  7347       1.959   1.953   0.170  1.00 20.00
> HETATM    3  C3  TRE  7347       2.717   1.276  -1.006  1.00 20.00
> HETATM    4  C4  TRE  7347       3.662   0.237  -0.355  1.00 20.00
> HETATM    5  C5  TRE  7347       2.806  -0.843   0.385  1.00 20.00
> HETATM    6  C6  TRE  7347       3.596  -1.917   1.069  1.00 20.00
> HETATM    7  O1  TRE  7347       0.133   0.432   0.010  1.00 20.00
> HETATM    8  O2  TRE  7347       1.086   2.923  -0.297  1.00 20.00
> HETATM    9  O3  TRE  7347       3.472   2.234  -1.665  1.00 20.00
> HETATM   10  O4  TRE  7347       4.408  -0.441  -1.302  1.00 20.00
> HETATM   11  O5  TRE  7347       1.964  -0.233   1.404  1.00 20.00
> HETATM   12  O6  TRE  7347       2.687  -2.806   1.676  1.00 20.00
> HETATM   13  C1P TRE  7347      -0.814  -0.557   0.430  1.00 20.00
> HETATM   14  C2P TRE  7347      -1.601  -1.752  -0.126  1.00 20.00
> HETATM   15  C3P TRE  7347      -2.572  -1.142  -1.231  1.00 20.00
> HETATM   16  C4P TRE  7347      -3.557  -0.224  -0.472  1.00 20.00
> HETATM   17  C5P TRE  7347      -2.743   0.960   0.225  1.00 20.00
> HETATM   18  C6P TRE  7347      -3.666   1.891   1.015  1.00 20.00
> HETATM   19  O2P TRE  7347      -0.693  -2.574  -0.755  1.00 20.00
> HETATM   20  O3P TRE  7347      -3.323  -2.155  -1.812  1.00 20.00
> HETATM   21  O4P TRE  7347      -4.483   0.363  -1.367  1.00 20.00
> HETATM   22  O5P TRE  7347      -1.775   0.343   1.115  1.00 20.00
> HETATM   23  O6P TRE  7347      -4.371   1.155   1.989  1.00 20.00
> REMARK TRE ENDHET
>
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------
> CIF
>
>
> # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to
> #          establish equivalence between model and topology. If
> #          you use O or other programmes that produce defective
> #          PDB files you must restore these columns, otherwise
> #          REFMAC5 will not recognise this topology.
> #
> #
> #       This file was generated by PRODRG version 071121.0636
> #       PRODRG written/copyrighted by Daan van Aalten
> #       and Alexander Schuettelkopf
> #
> #       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> #
> #       When using this software in a publication, cite:
> #       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> #       PRODRG - a tool for high-throughput crystallography
> #       of protein-ligand complexes.
> #       Acta Crystallogr. D60, 1355--1363.
> #
> #
> global_
> _lib_name         prodrg_lib
> _lib_version       71121
> _lib_update       ?
> #
> # ---------------
> #
> data_comp_list
> #
> loop_
> _chem_comp.id
> _chem_comp.three_letter_code
> _chem_comp.name
> _chem_comp.group
> _chem_comp.number_atoms_all
> _chem_comp.number_atoms_nh
> _chem_comp.desc_level
> TRE     TRE   'TRE              ' non-polymer        45  23 .
> #
> # ---------------
> #
> data_comp_TRE
> #
> loop_
> _chem_comp_atom.comp_id
> _chem_comp_atom.atom_id
> _chem_comp_atom.type_symbol
> _chem_comp_atom.type_energy
> _chem_comp_atom.partial_charge
>   TRE         O2     O    OH1      -0.115
>   TRE         HAA    H    HOH1      0.028
>   TRE         C2     C    CH1       0.074
>   TRE         1H2    H    HCH1      0.000
>   TRE         C3     C    CH1       0.074
>   TRE         1H3    H    HCH1      0.000
>   TRE         O3     O    OH1      -0.115
>   TRE         HAB    H    HOH1      0.028
>   TRE         C4     C    CH1       0.074
>   TRE         1H4    H    HCH1      0.000
>   TRE         O4     O    OH1      -0.115
>   TRE         HAC    H    HOH1      0.028
>   TRE         C5     C    CH1       0.126
>   TRE         1H5    H    HCH1      0.000
>   TRE         C6     C    CH2       0.037
>   TRE         1H6    H    HCH2      0.000
>   TRE         2H6    H    HCH2      0.000
>   TRE         O6     O    OH1      -0.115
>   TRE         HAD    H    HOH1      0.028
>   TRE         O5     O    O2       -0.109
>   TRE         C1     C    CH1       0.126
>   TRE         1H1    H    HCH1      0.000
>   TRE         O1     O    O2       -0.109
>   TRE         C1P    C    CH1       0.126
>   TRE         1H1P   H    HCH1      0.000
>   TRE         O5P    O    O2       -0.109
>   TRE         C5P    C    CH1       0.126
>   TRE         1H5P   H    HCH1      0.000
>   TRE         C6P    C    CH2       0.037
>   TRE         1H6P   H    HCH2      0.000
>   TRE         2H6P   H    HCH2      0.000
>   TRE         O6P    O    OH1      -0.115
>   TRE         HAH    H    HOH1      0.029
>   TRE         C4P    C    CH1       0.074
>   TRE         1H4P   H    HCH1      0.000
>   TRE         O4P    O    OH1      -0.115
>   TRE         HAG    H    HOH1      0.028
>   TRE         C3P    C    CH1       0.074
>   TRE         1H3P   H    HCH1      0.000
>   TRE         O3P    O    OH1      -0.115
>   TRE         HAF    H    HOH1      0.028
>   TRE         C2P    C    CH1       0.074
>   TRE         1H2P   H    HCH1      0.000
>   TRE         O2P    O    OH1      -0.115
>   TRE         HAE    H    HOH1      0.028
> loop_
> _chem_comp_tree.comp_id
> _chem_comp_tree.atom_id
> _chem_comp_tree.atom_back
> _chem_comp_tree.atom_forward
> _chem_comp_tree.connect_type
>   TRE      O2     n/a    C2     START
>   TRE      HAA    O2     .      .
>   TRE      C2     O2     C1     .
>   TRE      1H2    C2     .      .
>   TRE      C3     C2     C4     .
>   TRE      1H3    C3     .      .
>   TRE      O3     C3     HAB    .
>   TRE      HAB    O3     .      .
>   TRE      C4     C3     C5     .
>   TRE      1H4    C4     .      .
>   TRE      O4     C4     HAC    .
>   TRE      HAC    O4     .      .
>   TRE      C5     C4     O5     .
>   TRE      1H5    C5     .      .
>   TRE      C6     C5     O6     .
>   TRE      1H6    C6     .      .
>   TRE      2H6    C6     .      .
>   TRE      O6     C6     HAD    .
>   TRE      HAD    O6     .      .
>   TRE      O5     C5     .      .
>   TRE      C1     C2     O1     .
>   TRE      1H1    C1     .      .
>   TRE      O1     C1     C1P    .
>   TRE      C1P    O1     C2P    .
>   TRE      1H1P   C1P    .      .
>   TRE      O5P    C1P    C5P    .
>   TRE      C5P    O5P    C4P    .
>   TRE      1H5P   C5P    .      .
>   TRE      C6P    C5P    O6P    .
>   TRE      1H6P   C6P    .      .
>   TRE      2H6P   C6P    .      .
>   TRE      O6P    C6P    HAH    .
>   TRE      HAH    O6P    .      .
>   TRE      C4P    C5P    C3P    .
>   TRE      1H4P   C4P    .      .
>   TRE      O4P    C4P    HAG    .
>   TRE      HAG    O4P    .      .
>   TRE      C3P    C4P    O3P    .
>   TRE      1H3P   C3P    .      .
>   TRE      O3P    C3P    HAF    .
>   TRE      HAF    O3P    .      .
>   TRE      C2P    C1P    O2P    .
>   TRE      1H2P   C2P    .      .
>   TRE      O2P    C2P    HAE    .
>   TRE      HAE    O2P    .      END
>   TRE      O5     C1     .      ADD
>   TRE      C3P    C2P    .      ADD
> loop_
> _chem_comp_bond.comp_id
> _chem_comp_bond.atom_id_1
> _chem_comp_bond.atom_id_2
> _chem_comp_bond.type
> _chem_comp_bond.value_dist
> _chem_comp_bond.value_dist_esd
>   TRE      O2     HAA       single      1.000    0.027
>   TRE      O2     C2        single      1.430    0.025
>   TRE      C2     C3        single      1.530    0.025
>   TRE      C2     C1        single      1.530    0.025
>   TRE      C3     O3        single      1.430    0.025
>   TRE      C3     C4        single      1.530    0.025
>   TRE      O3     HAB       single      1.000    0.027
>   TRE      C4     O4        single      1.430    0.025
>   TRE      C4     C5        single      1.530    0.025
>   TRE      O4     HAC       single      1.000    0.027
>   TRE      C5     C6        single      1.530    0.033
>   TRE      C5     O5        single      1.435    0.033
>   TRE      C6     O6        single      1.430    0.025
>   TRE      O6     HAD       single      1.000    0.027
>   TRE      O5     C1        single      1.435    0.033
>   TRE      C1     O1        single      1.435    0.033
>   TRE      O1     C1P       single      1.435    0.033
>   TRE      C1P    O5P       single      1.435    0.033
>   TRE      C1P    C2P       single      1.530    0.025
>   TRE      O5P    C5P       single      1.435    0.033
>   TRE      C5P    C6P       single      1.530    0.033
>   TRE      C5P    C4P       single      1.530    0.025
>   TRE      C6P    O6P       single      1.430    0.025
>   TRE      O6P    HAH       single      1.000    0.027
>   TRE      C4P    O4P       single      1.430    0.025
>   TRE      C4P    C3P       single      1.530    0.025
>   TRE      O4P    HAG       single      1.000    0.027
>   TRE      C3P    O3P       single      1.430    0.025
>   TRE      C3P    C2P       single      1.530    0.025
>   TRE      O3P    HAF       single      1.000    0.027
>   TRE      C2P    O2P       single      1.430    0.025
>   TRE      O2P    HAE       single      1.000    0.027
>   TRE      C2     1H2       single      1.000    0.020
>   TRE      C3     1H3       single      1.000    0.020
>   TRE      C4     1H4       single      1.000    0.020
>   TRE      C5     1H5       single      1.000    0.020
>   TRE      C6     1H6       single      1.000    0.020
>   TRE      C6     2H6       single      1.000    0.020
>   TRE      C1     1H1       single      1.000    0.020
>   TRE      C1P    1H1P      single      1.000    0.020
>   TRE      C5P    1H5P      single      1.000    0.020
>   TRE      C6P    1H6P      single      1.000    0.020
>   TRE      C6P    2H6P      single      1.000    0.020
>   TRE      C4P    1H4P      single      1.000    0.020
>   TRE      C3P    1H3P      single      1.000    0.020
>   TRE      C2P    1H2P      single      1.000    0.020
> loop_
> _chem_comp_angle.comp_id
> _chem_comp_angle.atom_id_1
> _chem_comp_angle.atom_id_2
> _chem_comp_angle.atom_id_3
> _chem_comp_angle.value_angle
> _chem_comp_angle.value_angle_esd
>   TRE      HAA    O2     C2      109.500    3.158
>   TRE      O2     C2     C3      109.500    2.727
>   TRE      O2     C2     C1      109.500    2.727
>   TRE      C3     C2     C1      111.000    2.727
>   TRE      C2     C3     O3      109.500    2.727
>   TRE      C2     C3     C4      111.000    2.727
>   TRE      O3     C3     C4      109.500    2.727
>   TRE      C3     O3     HAB     109.500    3.158
>   TRE      C3     C4     O4      109.500    2.727
>   TRE      C3     C4     C5      111.000    2.727
>   TRE      O4     C4     C5      109.500    2.727
>   TRE      C4     O4     HAC     109.500    3.158
>   TRE      C4     C5     C6      109.500    5.000
>   TRE      C4     C5     O5      109.500    4.412
>   TRE      C6     C5     O5      109.500    4.412
>   TRE      C5     C6     O6      109.500    2.727
>   TRE      C6     O6     HAD     109.500    3.158
>   TRE      C5     O5     C1      109.500    3.750
>   TRE      C2     C1     O5      109.500    4.412
>   TRE      C2     C1     O1      109.500    4.412
>   TRE      O5     C1     O1      109.500    4.412
>   TRE      C1     O1     C1P     109.500    3.750
>   TRE      O1     C1P    O5P     109.500    4.412
>   TRE      O1     C1P    C2P     109.500    4.412
>   TRE      O5P    C1P    C2P     109.500    4.412
>   TRE      C1P    O5P    C5P     109.500    3.750
>   TRE      O5P    C5P    C6P     109.500    4.412
>   TRE      O5P    C5P    C4P     109.500    4.412
>   TRE      C6P    C5P    C4P     109.500    5.000
>   TRE      C5P    C6P    O6P     109.500    2.727
>   TRE      C6P    O6P    HAH     109.500    3.158
>   TRE      C5P    C4P    O4P     109.500    2.727
>   TRE      C5P    C4P    C3P     111.000    2.727
>   TRE      O4P    C4P    C3P     109.500    2.727
>   TRE      C4P    O4P    HAG     109.500    3.158
>   TRE      C4P    C3P    O3P     109.500    2.727
>   TRE      C4P    C3P    C2P     111.000    2.727
>   TRE      O3P    C3P    C2P     109.500    2.727
>   TRE      C3P    O3P    HAF     109.500    3.158
>   TRE      C1P    C2P    C3P     111.000    2.727
>   TRE      C1P    C2P    O2P     109.500    2.727
>   TRE      C3P    C2P    O2P     109.500    2.727
>   TRE      C2P    O2P    HAE     109.500    3.158
>   TRE      O2     C2     1H2     109.500    3.300
>   TRE      C2     C3     1H3     109.500    3.300
>   TRE      C3     C4     1H4     109.500    3.300
>   TRE      C4     C5     1H5     109.500    3.300
>   TRE      C5     C6     1H6     109.500    3.300
>   TRE      C5     C6     2H6     109.500    3.300
>   TRE      C2     C1     1H1     109.500    3.300
>   TRE      O1     C1P    1H1P    109.500    3.300
>   TRE      O5P    C5P    1H5P    109.500    3.300
>   TRE      C5P    C6P    1H6P    109.500    3.300
>   TRE      C5P    C6P    2H6P    109.500    3.300
>   TRE      C5P    C4P    1H4P    109.500    3.300
>   TRE      C4P    C3P    1H3P    109.500    3.300
>   TRE      C1P    C2P    1H2P    109.500    3.300
> loop_
> _chem_comp_tor.comp_id
> _chem_comp_tor.id
> _chem_comp_tor.atom_id_1
> _chem_comp_tor.atom_id_2
> _chem_comp_tor.atom_id_3
> _chem_comp_tor.atom_id_4
> _chem_comp_tor.value_angle
> _chem_comp_tor.value_angle_esd
> _chem_comp_tor.period
>   TRE      var_001   C1     C2     O2     HAA       60.000   13.333   3
>   TRE      CONST_001 C4     C3     C2     O2        60.000    0.714   3
>   TRE      CONST_002 O2     C2     C1     O1        60.000    0.714   3
>   TRE      var_002   C2     C3     O3     HAB       60.000   13.333   3
>   TRE      CONST_003 C5     C4     C3     C2        60.000    0.714   3
>   TRE      var_003   C3     C4     O4     HAC       60.000   13.333   3
>   TRE      CONST_004 C3     C4     C5     O5        60.000    0.714   3
>   TRE      var_004   C4     C5     C6     O6        60.000    2.857   3
>   TRE      CONST_005 C4     C5     O5     C1        60.000    1.111   3
>   TRE      var_005   C5     C6     O6     HAD       60.000   13.333   3
>   TRE      CONST_006 O1     C1     O5     C5        60.000    1.111   3
>   TRE      var_006   C2     C1     O1     C1P       60.000    4.444   3
>   TRE      var_007   C2P    C1P    O1     C1        60.000    4.444   3
>   TRE      CONST_007 O1     C1P    O5P    C5P       60.000    1.111   3
>   TRE      CONST_008 O1     C1P    C2P    O2P       60.000    0.714   3
>   TRE      CONST_009 C4P    C5P    O5P    C1P       60.000    1.111   3
>   TRE      var_008   O5P    C5P    C6P    O6P       60.000    2.857   3
>   TRE      CONST_010 O5P    C5P    C4P    C3P       60.000    0.714   3
>   TRE      var_009   C5P    C6P    O6P    HAH       60.000   13.333   3
>   TRE      var_010   C5P    C4P    O4P    HAG       60.000   13.333   3
>   TRE      CONST_011 C2P    C3P    C4P    C5P       60.000    0.714   3
>   TRE      var_011   C4P    C3P    O3P    HAF       60.000   13.333   3
>   TRE      CONST_012 O2P    C2P    C3P    C4P       60.000    0.714   3
>   TRE      var_012   C1P    C2P    O2P    HAE       60.000   13.333   3
> loop_
> _chem_comp_chir.comp_id
> _chem_comp_chir.id
> _chem_comp_chir.atom_id_centre
> _chem_comp_chir.atom_id_1
> _chem_comp_chir.atom_id_2
> _chem_comp_chir.atom_id_3
> _chem_comp_chir.volume_sign
>   TRE      chir_001  C2     O2     C3     C1        positiv
>   TRE      chir_002  C3     C2     C4     O3        positiv
>   TRE      chir_003  C4     C3     O4     C5        positiv
>   TRE      chir_004  C5     C4     O5     C6        positiv
>   TRE      chir_005  C1     C2     O5     O1        positiv
>   TRE      chir_006  C1P    O1     C2P    O5P       positiv
>   TRE      chir_007  C5P    O5P    C6P    C4P       positiv
>   TRE      chir_008  C4P    C5P    C3P    O4P       positiv
>   TRE      chir_009  C3P    C4P    O3P    C2P       positiv
>   TRE      chir_010  C2P    C1P    O2P    C3P       positiv
> #
> # ---------------
> #
>
>
> ____________________________________________________________________
> Ruben Van der Meeren
> Bachelor in biochemistry and biotechnology
> Adress:  de Pretlaan 26, B9850 Nevele
> Tel.:  +32478/217480
> E-Mail:  ruben.vandermeeren at mac.com; ruben.vandermeeren at ugent.be
> URL:  http://web.mac.com/ruben.vandermeeren
> iChat: ruben.vandermeeren at mac.com
> Skype: ruben_van_der_meeren
>
>
>
>
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> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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>   




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