Thanks for the reply. very well i agree with what you have to say. however in that case the answer which i am getting for other options claiming that the lsq fit say for backbone is 0.98732 so on ., are useless values. now again if that is the case shoukld i assume that native structure RMSD calculations using g_confrms_d is invalid.
David i hope this question of mine making sense. plz clarify if i am missing something important. everyone is performing rmsd calculations on proteins, what is that i am doing wrong here. thanks.
Arindam Ganguly
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