[phenixbb] sugar chain cif file

Nigel W. Moriarty nwmoriarty at lbl.gov
Tue Jul 8 09:00:19 PDT 2008


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
>
>
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov




More information about the phenixbb mailing list