Re: [modeller_usage] MSE query

[Modeller Caretaker <>]

On 4/8/11 9:45 PM,  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
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