Hello all, Being a novice in this field, I have a rudimentary question re: Superpose results. I did an alignment using Superpose of a liganded protein with the native protein (2 molecules in the ASU). BEcause it was the same protein I used the default to do an atom-by-atom superimposition. I also did an alighment using SSM with the same protein in a different species (which seemed logical to me at the time since they are similar but not identical sequences). In any case, with SSM, the analysis gives you an rmsd value which I believe is typical. However for my atom-by-atom alignment, the values reported are RMS B DISPLACEMENT, AVERAGE B DISPLACEMENT RMS XYZ DISPLACEMENT AVERAGE XYZ DISPLACEMENT MAXIMUM XYZ DISPLACEMENT
For me this was useful as I could pinpoint where the major change was upon binding of ligand as well as give the closeness of the alignment. However, I was told that generally one would report an rmsd value rather than rms, average, and maximum displacement. So, my question is: Is the rms xyz displacement equivalent to an rmsd? If not, can one calculate the rmsd from the results of the analysis. What is the typical way one would report the results of this analysis. Thank you very much for your patience. Mona Rahman --------------------------------------------------- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology & Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
