It seems there are some differences with respect to non-standard residues between Modeller4 and Modeller6v2. I'm working on conotoxin. Some conotoxin sequences include non-standard residues. (such as 1OMC.pdb includes HYP) When I used Modeller4 before, I modified the template file("HETATM" into "ATOM "), then did alignment and modelling. The non-standard residues were read as "B". I'm currently using Modeller6v2. When I did the same things, these residues were read as "G". So the program always complain "the sequence is different with structure." Maybe a dirty solution is : modify the template file, delete surplus atoms, change the non-standard residue into standard residue. But non-standard residues are important for the function of conotoxin. Is there a better way to deal with non-standard residues? It seems that "SET HETATM_IO=ON" can not solve this problem. Thank you very much! With best regards, Kong Lesheng

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