Messages

1

General discussions (Q&As) / Re: general questions about SNAP- rotation parameters

« on: March 01, 2012, 05:52:39 pm »

thanks!
I followed the "technical details" and did the calculation.
Here is the recap

.par data
   C111.A-D218.T:A5.ARG 9ant.mod.pdb +   -10.7995   25.8394
   -10.6263    1.2572    1.4595    8.3168  -24.2450    3.2969
   -10.7362    0.9216   -0.7160
    0.9104    0.0245    0.4130
   -0.0849    0.9881    0.1285
   -0.4050   -0.1521    0.9016
  -10.7447    0.9360   -0.7120

My results...
Frame origin
   .par file (line 2) -10.7362    0.9216   -0.7160
   Calculation- -10.73679 0.9216302 -0.7163861

x-, y- and z- axes
   .par file
0.9104    0.0245    0.4130
-0.0849    0.9881    0.1285
 -0.4050   -0.1521    0.9016

Calculation
0.91042237  0.02449907 0.4129539
-0.08481114  0.98809458 0.1283595
-0.40489280 -0.15188448 0.9016612

I used "R" to do the calculation. Attached is the details of my calculation.

2

General discussions (Q&As) / Re: general questions about SNAP- rotation parameters

« on: March 01, 2012, 01:45:31 pm »

Thanks! got it!

3

General discussions (Q&As) / Re: general questions about SNAP- rotation parameters

« on: March 01, 2012, 01:21:24 pm »

Thanks a lot!
For example
(0) B7.A:A142.ALA /home/xiangjun/SNAP/dataset/TAR/1ckq.mod.pdb -     6.3860 -137.3112
(1)   -5.3859    3.3886    0.5394   45.1364   74.4956 -119.7086
(2)    0.1860    4.2367    4.7746
(3)   -0.4801   -0.0354   -0.8765
(4)    0.8770   -0.0405   -0.4787
(5)   -0.0186   -0.9985    0.0505
(6)    0.1760    4.2555    4.7747

In my understanding
Line 1- Six rigid body parameters; translation distance + rotation distance (describing the relative distance between origin of AA coordinate system and base -pair ones?)
Line 2- AA frame origin (sets as the reference frame when superimposing those same AA?)
Line 3- X-axis coordinates for C, N, CB atoms ? OR the x-vector (Ca- Cb) in AA reference frame?

Thanks

4

General discussions (Q&As) / Re: general questions about SNAP- rotation parameters

« on: February 23, 2012, 01:32:24 pm »

Thanks a lot That makes sense.

Well I did not quite understand the R matrix. In my understanding, we define the "middle frame" for the base pair based on this R matrix. Then we can describe the position of atoms in a base pair, using the same set of parameters. Meanwhile the 6 parameters in .par file describes the relative relationship between C alpha atom and the origin of the "middle frame". The coordinates of the CB, N, O in .par file describing the position within the AA reference frame.  Is it right? Thanks again! 

5

General discussions (Q&As) / general questions about SNAP- rotation parameters

« on: February 20, 2012, 03:21:59 pm »

Hi

I am a beginner in SNAP. I have a general questions about the par file format. Thanks!

(0) B7.A:A142.ALA /home/xiangjun/SNAP/dataset/TAR/1ckq.mod.pdb -     6.3860 -137.3112
(1)   -5.3859    3.3886    0.5394   45.1364   74.4956 -119.7086
(2)    0.1860    4.2367    4.7746
(3)   -0.4801   -0.0354   -0.8765
(4)    0.8770   -0.0405   -0.4787
(5)   -0.0186   -0.9985    0.0505
(6)    0.1760    4.2555    4.7747

As it's indicated, line 1 shows the 3 translation parameters and 3 rotation parameters of C alpha atom.  In my understanding, the rotation parameters refer to the minimum rotation angle needed to superimpose the two local coordinate systems (base pair and amino acids). But what are the exactly definitions for them? Do they correspond to buckle, propeller and opening parameters? In the Siggers (2005) paper, they only used delta a and delta theta  describing the rotation angle. How does SNAP calculate the third rotation parameter? Also I tried calculating the distances and measuring the dissimilarities among different C alpha atoms I happened to find that the number of the last rotation parameter is the largest one among the total 6 parameters. Is it coincidence? Thanks again!

Bests