The question: "We are having problem with mutate_insert command. It used to work, then I was using 5.9.1 version. Now, it does not seem to work. I followed the instructions in ofaq and o-for-morons. Are there any changes in the sequence of commands, or am I missing something. Could any one let me know step-by-step instruction to get mutate_insert to work?. Thanks for any suggestion/help. Ps: I am trying to add residues at the end of c-terminus. The ofaq suggests to do lego_loop. Do I include the new residue in the lego_loop search?."
Satish Nair replied: One thing you may want to check is the environmental definitions for your o directories. They should have things in small letters (for example /disk2/O is bad but /disk2/o works fine). Otherwise, you may want to check mutate_setup or see if the connectivity file (all.dat) is defined correctly (using the connect command in o). The new inserted residues will be included in the lego_loop search.
Alwyn added: There is no change in the mutate commands. If you have a problem, please describe it in more detail, sending it just to me. Nowadays i would build the inserted bits (and the neighbouring residues) with the baton commands if i had some density to go by, otherwise i'd play with the lego_loop commands and pray.