Paul Emsley wrote:
For the record, the copy of the Refmac library that you get with a Coot
binary tar file unfortunately does not contain the CYS-BME. AFAICS, the
Refmac library that comes with CCP4 6.1 does not contain CYS-BME either.
You can build your own version of the CYS-BME using CYS-MPR (the
propionate form) as a template.
However, when you have done that, I doubt that Coot will handle the link
properly - I'll see what I can do about that.
Attached is a CYS-BME link description. It works fine in Coot rev 1775
- perhaps less well in previous revs. You will need to use the
refine-residues function for the link to be found.
Paul.
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
CYS-BME BME . . CYS . . SS-bridge
data_link_CYS-BME
#
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
CYS-BME 1 S2 2 SG single 2.031 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
CYS-BME 1 C2 1 S2 2 SG 110.000 3.000
CYS-BME 1 S2 2 SG 2 CB 110.000 3.000
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
CYS-BME ss 1 C2 1 S2 2 SG 2 CB 90.00 10.0 2
#
