Hello there
How do I tell Refmac that I have an inhibitor covalently bound to a Ser
residue? I am using the ccp4i interface and this is what I've came up
with (looking through the archives) but it does not seem to work
1) I made the inhibitor mon_lib.cif
2) I made the following mon_link.cif
# ------------------------------------------------
# --- LIST OF LINKS ---
#
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
SER-LIG SER . . LIG . .
bond_SER-OG=_LIG-C8
# ------------------------------------------------------
#
# --- DESCRIPTION OF LINKS ---
#
data_link_SER-LIG
#
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
SER-LIG 1 OG 2 C8 coval 1.330 0.200
# ------------------------------------------------------
3) I inserted in the PDB header the following line
LINK OG SER A 90 C8 LIG L 1
SER-LIG
If I generate a single lig.cif file from the Mon_lib and the Link_lib
and I read it using the "Library" option in the GUI, Refmac failes with
a floating error. If I read the mon_lib ONLY trhough the GUI, it works,
it finds the link, it says that the bond should be 1.33 Ang, but in the
final coordinates the bond is 1.75 (starting model was 1.5); f I read
the mon_lib trhough the GUI, AND the link_lib using the developer
option....same story.
I am at a loss, any suggestion would be welcome. Thanks a lot
Giovanna
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