I am asking this question on behalf of a friend: -Thanks!
Hi All - I am working at small biotech. We have minimal budget for software, only CCP4 and Coot. We have a ligand that binds covalently to cysteine. I define the parameter file using Prodrg in CCP4 to get drug.cif file and then make a link in Coot between the Cys and the Drug. The problem is Refmac keeps complaining that there is no link_id for this bond: I am reading library. Please wait. mon_lib.cif WARNING : link: CYS<-->UNK is without link_id link will be created with covalent bond only. Bond= 1.610 WARNING : description of link:CYS-UNK is not in the dictionary link will be created with bond_length = 1.610 Where do I specify this link_id, and where can I find an example for the correct syntax? Is this done in mon_lib.cif or the drug.cif file?? The bond length, if I'm not mistaken should be ~1.82 A for distance between carbon and sulfur. Thanks for any help.
