[phenixbb] sugar chain cif file
Pavel Afonine
pafonine at lbl.gov
Tue Jul 8 09:47:51 PDT 2008
Another way of doing this is to define bond and angle manually. Look
here for more information and example:
http://phenix-online.org/documentation/refinement.htm#anch290
Pavel.
On 7/8/2008 9:00 AM, Nigel W. Moriarty wrote:
> Daniele
>
> eLBOW can generate the CIF links if put LINK records in the input PDB
> file. Otherwise you can follow the example here.
>
> http://phenix-online.org/documentation/refinement.htm#anch281
>
> Please contact me if you have any more trouble.
>
> Nigel
>
> On 7/8/2008 8:43 AM, Daniele de Sanctis wrote:
>
>> Dear all,
>>
>> I have a trisaccharide in my structure, and I generate the cif file
>> with elbow (see below). Unfortunately phenix.refine seems not
>> recognizing the bonds C5-O1 between different units and is not keeping
>> the chain together. As far as I could understand I should also use the
>> keyword "apply_cif_link", but I couldn't find which syntax i should
>> use.
>>
>> Thanks for the help
>>
>> Daniele
>>
>> # electronic Ligand Builder and Optimisation Workbench (eLBOW)
>> # - a module of PHENIX version 1.3b (Mon Nov 20 17:20:00 2007)
>> # - file written: Mon Jul 7 18:19:22 2008
>> #
>> # Input file: a3.pdb
>> #
>> 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
>> AHR AHR 'Unknown ' ligand 15 9 .
>> #
>> data_comp_AHR
>> #
>> 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
>> _chem_comp_atom.x
>> _chem_comp_atom.y
>> _chem_comp_atom.z
>> AHR 'C5'' C CH3 . 61.3311 15.7148 36.7946
>> AHR 'C4'' C CR5 . 60.1817 16.4682 36.1126
>> AHR 'O4'' O O . 60.3257 17.5507 35.0934
>> AHR 'C3'' C CR5 . 58.6911 16.2438 36.3556
>> AHR 'O3'' O OC . 58.1296 15.2877 37.2130
>> AHR 'C2'' C CR5 . 57.9427 17.1885 35.4852
>> AHR 'O2'' O OC . 56.5500 17.3383 35.4371
>> AHR 'C1'' C CR5 . 58.9640 18.0045 34.6971
>> AHR 'O1'' O OH1 . 58.6701 18.9985 33.7515
>> AHR 'H5'1' H HCH3 . 61.2131 14.6537 36.6320
>> AHR 'H5'2' H HCH3 . 61.3175 15.9201 37.8548
>> AHR 'H5'3' H HCH3 . 62.2726 16.0401 36.3773
>> AHR 'H3'1' H H . 57.7021 15.7812 38.0734
>> AHR 'H2'1' H H . 56.1521 16.7529 34.6214
>> AHR 'H1'1' H HOH1 . 59.4063 19.7861 33.8153
>> #
>> 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
>> AHR 'C5'' 'C4'' single 1.53429 0.02
>> AHR 'C4'' 'O4'' aromatic 1.49380 0.02
>> AHR 'C4'' 'C3'' aromatic 1.52685 0.02
>> AHR 'O4'' 'C1'' aromatic 1.48900 0.02
>> AHR 'C3'' 'O3'' double 1.40168 0.02
>> AHR 'C3'' 'C2'' aromatic 1.48663 0.02
>> AHR 'C2'' 'O2'' double 1.40154 0.02
>> AHR 'C2'' 'C1'' aromatic 1.52635 0.02
>> AHR 'C1'' 'O1'' single 1.40306 0.02
>> AHR 'H5'1' 'C5'' single 1.08000 0.02
>> AHR 'H5'2' 'C5'' single 1.08000 0.02
>> AHR 'H5'3' 'C5'' single 1.08000 0.02
>> AHR 'H3'1' 'O3'' single 1.08000 0.02
>> AHR 'H2'1' 'O2'' single 1.08000 0.02
>> AHR 'H1'1' 'O1'' single 1.08000 0.02
>> #
>> 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
>> AHR 'O4'' 'C4'' 'C5'' 125.93952 3.0
>> AHR 'C3'' 'C4'' 'C5'' 126.05117 3.0
>> AHR 'H5'1' 'C5'' 'C4'' 109.48717 3.0
>> AHR 'H5'2' 'C5'' 'C4'' 109.48699 3.0
>> AHR 'H5'3' 'C5'' 'C4'' 109.47730 3.0
>> AHR 'C1'' 'O4'' 'C4'' 108.31507 3.0
>> AHR 'O3'' 'C3'' 'C4'' 126.06060 3.0
>> AHR 'C2'' 'C3'' 'C4'' 107.75208 3.0
>> AHR 'C3'' 'C4'' 'O4'' 108.00930 3.0
>> AHR 'C2'' 'C1'' 'O4'' 108.15545 3.0
>> AHR 'O1'' 'C1'' 'O4'' 125.92746 3.0
>> AHR 'H3'1' 'O3'' 'C3'' 109.52327 3.0
>> AHR 'O2'' 'C2'' 'C3'' 126.02920 3.0
>> AHR 'C1'' 'C2'' 'C3'' 107.76809 3.0
>> AHR 'C2'' 'C3'' 'O3'' 126.15656 3.0
>> AHR 'H2'1' 'O2'' 'C2'' 109.52075 3.0
>> AHR 'O1'' 'C1'' 'C2'' 125.91301 3.0
>> AHR 'C1'' 'C2'' 'O2'' 126.15898 3.0
>> AHR 'H1'1' 'O1'' 'C1'' 109.51700 3.0
>> AHR 'H5'2' 'C5'' 'H5'1' 109.46605 3.0
>> AHR 'H5'3' 'C5'' 'H5'1' 109.45474 3.0
>> AHR 'H5'3' 'C5'' 'H5'2' 109.45508 3.0
>> #
>> 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
>> AHR CONST_01 'C2'' 'C1'' 'O4'' 'C4'' 0.00000 0.0 0
>> AHR CONST_02 'C1'' 'C2'' 'C3'' 'C4'' -0.00000 0.0 0
>> AHR CONST_03 'C2'' 'C3'' 'C4'' 'O4'' 0.00000 0.0 0
>> AHR CONST_04 'C3'' 'C2'' 'C1'' 'O4'' -0.00000 0.0 0
>> AHR CONST_05 'C1'' 'O4'' 'C4'' 'C3'' -0.00000 0.0 0
>> #
>> loop_
>> _chem_comp_plane_atom.comp_id
>> _chem_comp_plane_atom.plane_id
>> _chem_comp_plane_atom.atom_id
>> _chem_comp_plane_atom.dist_esd
>> AHR plan-1 'C4'' 0.020
>> AHR plan-1 'O4'' 0.020
>> AHR plan-1 'C1'' 0.020
>> AHR plan-1 'C2'' 0.020
>> AHR plan-1 'C3'' 0.020
>> AHR plan-1 'C5'' 0.050
>> AHR plan-1 'O1'' 0.050
>> AHR plan-1 'O2'' 0.050
>> AHR plan-1 'O3'' 0.050
>> AHR plan-2 'C4'' 0.100
>> AHR plan-2 'O4'' 0.100
>> AHR plan-2 'C5'' 0.100
>> AHR plan-2 'C3'' 0.100
>> AHR plan-3 'C3'' 0.100
>> AHR plan-3 'O3'' 0.100
>> AHR plan-3 'C4'' 0.100
>> AHR plan-3 'C2'' 0.100
>> AHR plan-4 'C2'' 0.100
>> AHR plan-4 'O2'' 0.100
>> AHR plan-4 'C3'' 0.100
>> AHR plan-4 'C1'' 0.100
>>
>>
>>
>>
>
>
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