Q1) Rms xyz and rmsd mean exactly the same . And as for what you should
report - that depends on the problem. As long as you state clearly what
has been fitted ( all atoms, CAs, loops excluded etc etc )
Q2) The algorithms for SSM and LSQKAB are different - SSM fits secondary
structure elements only, then checks the rmsd of all CAs. This is
particularly useful for fitting homolous proteins.
LSQKAB requires a list of all the atoms to be matched and that "rms
xyz" considers all those atoms and only those.
If you want a report of all differences you must click for that on the GUI.
And as you say this is helpful for finding differences in different
copies of the same molecule.
Eleanor
Mona Rahman wrote:
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]
