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