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 ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------
