Hi,
On 11/20/13, 4:17 PM, Zhijie Li wrote:
If you need to refine the structure with phenix.refine then you need
to make an edit file to specify that the mannose C1 is linked to the
ser OG by a covalent bond.
I am not sure if this is what was meant, but you don't need to define
bonds explicitly in phenix. Phenix.refine has the same (or a forked
version, I am not sure) monomer library as refmac's, and it contains the
MAN-SER and MAN-THR linkages, which includes bond distance and angle
restraints, but no torsion angles (see below). You can invoke a MAN-SER
or MAN-THR linkage from the phenix.refine GUI, or add a parameter file
to define it. You shouldn't need to specify distances and angles. I am
guessing the not-fully mature linkage-detection function in phenix,
which works well for N-linked sugars, might also work for O-linked, but
Nigel Moriarty from the PHENIX team would know (looking forward to this
being automatic).
By the way, this is how MAN-SER looks in the latest phenix monomer library:
#
data_link_MAN-SER
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
MAN-SER 1 C1 2 OG single 1.439 0.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
MAN-SER 1 C1 2 OG 2 CB 108.700 3.000
MAN-SER 1 O5 1 C1 2 OG 112.300 3.000
Engin
