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