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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
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