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[modeller_usage] building missing residues





Hi,

a protein i am dealing with has some missing residues. I am trying to build it with modeller. How could i verify the structure generated?
Also the remarks says, CA 5% of the side chains are poorly defined and are currently modelled as alanines.
Do any one know the meaning of this remark. Should i do any thing as part of correcting the structure for md simulation?