[phenixbb] Exploded ligands and phenix...
Ruben Van der Meeren
ruben.vandermeeren at ugent.be
Tue Apr 28 05:04:01 PDT 2009
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
More information about the phenixbb
mailing list