[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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