Re: [modeller_usage] MSE query

On 4/8/11 9:45 PM, rjayashree13-science@yahoo.co.in wrote: > I have a question about selenomethionine residues in PDB file. In the > original sequence file, these are methionine residues but in PDB these > are selenomethionine. I am using this PDB structure as a template. Can > you suggest what is to be done about these residues?

When Modeller reads in your template PDB file, it will automatically translate any selenomethionine residues to regular methionine. See http://salilab.org/modeller/9.9/manual/node171.html

Thus, use the regular methionine 'M' one-letter code in your alignment for these residues.

Ben Webb, Modeller Caretaker