I tried to do homology modelling using MODELLER and I calculate the RMSD value of the template structure and the model result using PyMol. The result shows "Executive: RMSD = 0.100 (241 to 241 atoms)". I want to know whether 0.100 is in armstrong or nm? Is this value acceptable or should I do another modelling? Please help me, thank you.
Only 290 atoms were aligned, which?
RMSD is in Angstroms. 0.1 Angstroms is very low but it does not mean that the model is accurate. Every model is acceptable until proven otherwise. RMSD metric does not provide such a proof.
What's the reason you measure the rmsd between your model and the template used??? There's no question that the folding of the model and its template is very close.
You should have a look into the similarity between their amino acid sequences or any other common features - except the folding term.
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