Dear All,

Does anyone know the exact meaning of the output from the first rigimol processing step?

For instance, if I give the rigimol program two structures that are very similar (structure #1 and structure #2), the program identifies several domains and gives the following output:

Rotations and Translations
Domain  RMSD         Axis         Angle      Translation     Distance
   1   0.19 ( 0.17, 0.26, 0.91)   -0.00  ( 0.00,-0.00,-0.00)   0.00
   2   0.17 (-0.65, 0.13, 0.74)    0.35  ( 0.04, 0.06,-0.03)   0.08
   3   0.21 ( 0.33, 0.33, 0.82)   -0.19  (-0.03,-0.03,-0.04)   0.06
   4   0.20 ( 0.49, 0.41, 0.61)    0.27  (-0.02, 0.02,-0.06)   0.06
   5   0.14 ( 0.40, 0.04, 0.92)   16.41  (-0.74, 0.36, 0.20)   0.85
   6   0.20 (-0.51,-0.47, 0.48)   23.92  (-0.39,-0.09,-1.21)   1.27
   7   0.51 ( 0.61,-0.15, 0.82)  -67.57  ( 1.27, 0.40,-0.49)   1.42
   8   0.04 ( 0.11,-0.14, 0.99)  113.72  ( 0.58,-0.07,-0.09)   0.59
   9   0.11 ( 0.02, 0.36, 0.85)  -65.37  (-0.28, 0.80,-0.62)   1.05
  10   0.05 (-0.67, 0.55, 0.36)   48.20  (-0.44,-1.14,-0.26)   1.25
  11   0.41 ( 0.73, 0.13, 0.85)  -88.51  (-0.22, 0.13,-0.11)   0.28
  12   0.02 (-0.17, 0.88,-0.39) -131.04  ( 0.07,-0.42,-0.43)   0.60
  13   0.02 (-0.46, 0.96,-0.05)  -86.21  ( 0.07, 0.03,-0.92)   0.92
  14   0.00 (-0.74, 0.23, 0.76) -111.08  (-1.16, 1.00,-0.61)   1.65

1. How meaningful is this output, if you'll excuse the rather vague question?

2. On a related thought, what exactly do the columns in the output mean? I can imagine that the RMSD is the root mean square deviation between domain 1 in structure #1 and domain 1 in structure #2.

3. What is the Axis column, and how is the axis defined? Also, what about the angle, and how is it defined? Is it the rotation of the domain about that axis from structure #1 to #2?

4. I'm guessing that the translation column gives the translation vector of the center (maybe center of mass) of the domain from structure #1 to #2. Am I right, and is the center the center of mass?


Thanks! and all the best,


--Buz


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