Thank you for your respones. I managed to fix the problem as follows:
Everytime I read in my dictionary from ccp4i Sketcher I got the "New ligand..." error and Refmac would write out a new .cif file. When I used the .cif file written by Refmac, refinement worked. I compared my Sketcher .cif and the .cif generated by Refmac. The difference I see between the two files is as follows:
Sketcher (under List of Monomers)
MOD MOD 'modified ' non-polymer 16 9 .
Refmac .cif (under List of Monomers)
MOD MOD '. ' . 15 9 .
MOD MOD 'modified ' non-polymer 16 9 .
If I add the extra line to the .cif I generated from Sketcher, it works! I'm glad I've got it running. Cheers! Catherine
Catherine Regni, Ph.D.
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