On 12/16/10 6:04 AM, Mike White wrote: > I am trying to model a small (22 amino acids) peptide with 3 > disulfide bonds using structures of 6 related peptides with Modeller > 9.7. The template peptides have 1-3 modified amino acids > (pyroglutamate, hydroxyproline, amidated C-termini) and the peptide > to be modeled has an amidated cysteine as the C-terminus.
Modeller cannot build models containing modified amino acids, nor can it use structural information from modified amino acids in your templates (the only exception is MSE, which Modeller treats as identical to MET).
Your best option in this case is to edit your template PDB file to convert the modified amino acids to their unmodified equivalents, build models with regular cysteine, and modify the C-terminus of the constructed models.
> I tried setting env.io.hetatm= True to see if that made a difference, > but then the routine failed with the following track back: ... > I'm not sure why env.io.hetatm = 'True' causes this error
True and 'True' are two different things. True is a Python boolean; 'True' is a string. Only the first will work here.
Ben Webb, Modeller Caretaker