[phenixbb] Problem with elbow
Subhani Bandara
ramssb17 at gmail.com
Thu Oct 25 08:54:22 PDT 2012
Dear all,
I am using the PHENIX version 1.8.1-1168 and need to get the pdb file and
the cif file for the metal-chelate complex Gd-DTPA for refinement of a
structure. I got the pdb file and the cif file for a dimer of the complex.
Then I edited those to contain only one metal chelator complex and used as
inputs in elbow. I have attached the pdb file and the cif file I used as
inputs.
I gave cif file as chemical file type with pdb file as initial geometry and
ran elbow. Then I used pdb file only or cif file only as inputs separately.
Every time it ended with the error “Failed to determine the bonding of a
fragment of the molecule”
Also I tried using smile string
C(CN(CC(=O)[O-])CC(=O)[O-])N(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Gd+3]and
pdb file as inputs. Then it runs without an error, but it outputs cif and
pdb files containing only Gd.
How can I get the cif file for the metal-chelate complex? I want to use
the metal-chelate complex as one entity in the refinement, so that it will
have the correct geometry of the chelator.
Thanks
Subhani
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###########################################################################
#
# Cambridge Crystallographic Data Centre
# CCDC
#
###########################################################################
#
# This CIF contains data generated directly from one or more entries in
# the Cambridge Structural Database and will include bibliographic,
# chemical, crystal, experimental, refinement, and atomic coordinate data,
# as available.
#
# Copyright 2012 The Cambridge Crystallographic Data Centre
#
# This CIF is provided on the understanding that it is used for bona fide
# research purposes only. It may contain copyright material of the CCDC
# or of third parties, and may not be copied or further disseminated in
# any form, whether machine-readable or not, except for the purpose of
# generating routine backup copies on your local computer system.
#
# For further information about the CCDC, data deposition and data
# retrieval see <www.ccdc.cam.ac.uk>. Bona fide researchers may freely
# download Mercury and enCIFer from this site to visualise CIF-encoded
# structures and to carry out CIF format checking respectively.
#
###########################################################################
data_CSD_CIF_YURCIX
_audit_creation_date 1996-05-02
_audit_creation_method CSD-ConQuest-V1
_database_code_CSD YURCIX
_chemical_formula_sum 'C28 H64 Gd2 N10 O26'
_chemical_formula_moiety
;
C14 Gd1 N3 O10
;
_journal_coden_Cambridge 155
_journal_volume 232
_journal_year 1995
_journal_page_first 203
_journal_name_full 'Inorg.Chim.Acta '
loop_
_publ_author_name
"M.B.Inoue"
"M.Inoue"
"Q.Fernando"
_chemical_name_systematic
;
Tetra-ammonium bis((\m~2~-diethylenetriaminepenta-acetato)-gadolinium)
hexahydrate
;
_cell_volume 1173.432
_exptl_crystal_density_diffrn 1.8
_diffrn_ambient_temperature ?
_diffrn_special_details
;
The study was carried out at room temperature,in the range 283-303K
;
_refine_special_details
;
Some water molecules have 0.5 occupancies.
;
#These two values have been output from a single CSD field.
_refine_ls_R_factor_gt 0.022
_refine_ls_wR_factor_gt 0.022
_symmetry_cell_setting triclinic
_symmetry_space_group_name_H-M 'P -1'
_symmetry_Int_Tables_number 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -x,-y,-z
_cell_length_a 10.121(7)
_cell_length_b 12.523(9)
_cell_length_c 9.767(7)
_cell_angle_alpha 105.893(2)
_cell_angle_beta 94.734(2)
_cell_angle_gamma 96.862(2)
_cell_formula_units_Z 1
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
Gd 1.79
N 0.68
O 0.68
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Gd1 Gd 0.12644(1) 0.19272(1) 0.21435(1)
O1 O 0.2195(3) 0.0873(2) 0.3619(3)
O2 O 0.2333(3) 0.0719(2) 0.5861(3)
O3 O 0.3406(2) 0.2599(2) 0.1623(3)
O4 O 0.5484(3) 0.3563(3) 0.2227(3)
O5 O 0.0873(3) 0.2364(2) -0.0075(2)
O6 O 0.1274(5) 0.3523(3) -0.1378(3)
O7 O 0.0187(3) 0.2245(2) 0.4246(3)
O8 O -0.1486(3) 0.2475(3) 0.5566(3)
O9 O -0.0568(2) 0.0410(2) 0.1308(3)
O10 O -0.2140(2) -0.0345(2) -0.0561(3)
N1 N 0.2931(3) 0.3114(2) 0.4438(3)
N2 N 0.1320(3) 0.4082(2) 0.2483(3)
N3 N -0.1263(3) 0.2456(2) 0.1867(3)
C1 C 0.2820(4) 0.2539(3) 0.5573(4)
C2 C 0.2423(4) 0.1279(3) 0.4964(4)
C3 C 0.4313(4) 0.3182(3) 0.4077(4)
C4 C 0.4410(3) 0.3115(3) 0.2524(4)
C5 C 0.2505(4) 0.4226(3) 0.4904(4)
C6 C 0.2358(4) 0.4754(3) 0.3701(4)
C7 C 0.1615(4) 0.4311(3) 0.1122(4)
C8 C 0.1219(4) 0.3329(3) -0.0216(4)
C9 C -0.0017(4) 0.4386(3) 0.2820(4)
C10 C -0.1156(4) 0.3623(3) 0.1762(4)
C11 C -0.1942(4) 0.2339(3) 0.3108(4)
C12 C -0.1023(3) 0.2357(3) 0.4407(4)
C13 C -0.1946(4) 0.1618(3) 0.0560(4)
C14 C -0.1520(3) 0.0477(3) 0.0427(3)
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
Gd1 O1 2.413 1_555 1_555
O1 C2 1.262 1_555 1_555
O2 C2 1.266 1_555 1_555
O3 Gd1 2.376 1_555 1_555
O4 C4 1.255 1_555 1_555
O5 Gd1 2.390 1_555 1_555
O6 C8 1.228 1_555 1_555
O7 Gd1 2.364 1_555 1_555
O8 C12 1.239 1_555 1_555
O9 Gd1 2.403 1_555 1_555
N1 Gd1 2.651 1_555 1_555
N2 Gd1 2.620 1_555 1_555
N3 Gd1 2.728 1_555 1_555
C1 N1 1.483 1_555 1_555
C2 C1 1.517 1_555 1_555
C3 N1 1.469 1_555 1_555
C4 O3 1.268 1_555 1_555
C5 N1 1.470 1_555 1_555
C6 N2 1.504 1_555 1_555
C7 N2 1.481 1_555 1_555
C8 O5 1.265 1_555 1_555
C9 N2 1.487 1_555 1_555
C10 N3 1.485 1_555 1_555
C11 N3 1.474 1_555 1_555
C12 O7 1.267 1_555 1_555
C13 N3 1.468 1_555 1_555
C14 O9 1.264 1_555 1_555
O10 C14 1.259 1_555 1_555
C3 C4 1.508 1_555 1_555
C5 C6 1.503 1_555 1_555
C7 C8 1.515 1_555 1_555
C9 C10 1.520 1_555 1_555
C11 C12 1.503 1_555 1_555
C13 C14 1.516 1_555 1_555
#END
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