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Author Topic: general questions about SNAP- rotation parameters  (Read 10164 times)

Offline Ming (Stacey)

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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

Offline xiangjun

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Re: general questions about SNAP- rotation parameters
« Reply #1 on: February 20, 2012, 04:19:11 pm »
The six parameters are just as "shear/stretch/stagger/buckle/propeller/opening" for base-pair parameters, and "shift/slide/rise/tilt/roll/twist" for the dinucleotide steps -- they quantify the spatial relationship rigorously between the side-chain reference frame and the base-pair reference frame. The technical details part (section #5) in the 3DNA manual contains a worked example on how to calculate step parameters. If you really want to get to the bottom of the matter, it's well worthwhile to repeat the example and try to understand every detail.

Quote
In the Siggers (2005) paper, they only used delta a and delta theta  describing the rotation angle.
Mathematically, to rigorously quantify the rotational relationship between two rigid bodies, three angular parameters are required. The Siggers method is a just an approximation, which may be sufficient for its purpose. To understand how the Siggers method works, you may need to dig into the source code -- simply reading the paper is not enough for the algorithmic details.

In light of this topic, you may want to pay more attention to the following quote:

Quote from: Siggers 2005 JMB paper
The approach used here is similar to that described by Pabo & Nekludova, but with two important differences. (1) Three geometric parameters [instead of two] are used in the comparison of residue-base-pairs, a feature that we found to increase the sensitivity of our analysis. ...

Xiang-Jun
« Last Edit: February 20, 2012, 04:28:55 pm by xiangjun »

Offline Ming (Stacey)

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Re: general questions about SNAP- rotation parameters
« Reply #2 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!  :)

Offline xiangjun

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Re: general questions about SNAP- rotation parameters
« Reply #3 on: February 23, 2012, 02:06:13 pm »
In the .par file, the so-called "R matrix" is actually the amino-acid-side-chain expressed when the corresponding base-pair reference frame is at [1 0 0; 0 1 0; 0 0 1] after coordinate transformation.

To verify, simply find the corresponding .pdb for a .par entry, and extract the xyz coordinates of both Cα and Cβ atoms. Then the unit vector of Cα→Cβ corresponds, approximately, to the x-axis (the first row of the "R-matrix"). Please post back an example.

Xiang-Jun
« Last Edit: February 23, 2012, 10:37:17 pm by xiangjun »

Offline Ming (Stacey)

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Re: general questions about SNAP- rotation parameters
« Reply #4 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 :)

Offline xiangjun

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Re: general questions about SNAP- rotation parameters
« Reply #5 on: March 01, 2012, 01:31:13 pm »
Please follow my last reply.

Xiang-Jun

Offline Ming (Stacey)

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Re: general questions about SNAP- rotation parameters
« Reply #6 on: March 01, 2012, 01:45:31 pm »
Thanks! got it!

Offline xiangjun

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Re: general questions about SNAP- rotation parameters
« Reply #7 on: March 01, 2012, 03:49:51 pm »
For reference, here is a note about .par file from SNAP.
>> Following our Monday meeting, I have updated the SNAP program to do what we 
>> have discussed. Specifically,
>>
>> [1] I have added a command line option -frame=NUMBER. By default, it now
>>    uses the CA-CB-N based reference frame for AA as used by Pabo and
>>    Siggers/Honig. The ls-fitting scheme applies equally well to GLYCINE
>>    since FOUR atoms (N/CA/C/CB) are used by default. For glycine, where
>>    CB is missing, the other three are used.
>>
>>    With -frame=1, the previous peptide based reference frame is used.
>>
>> [2] When deciding the contacts, only heavy atoms (i.e., non-Hs) are
>>    considered.
>>
>> [3] SNAP now ouputs 4 types of AA-bp interactions, controlled by the new
>>    command line option -type=NUMBER, as follows:
>>        0: with any atom -- EITHER base OR backbone atom
>>        1: with base atom (could also contact backbone, default)
>>        2: with backbone atom (could also contact base)
>>        3: must contact BOTH base AND backbone atom
>>    The output files are now named like
>>        AT-ALA_1.par, AT-ALA_1.pdb etc for type=1, i.e., contacting base
>>        for -type=2, it would be AT-ALA_2.par etc, and so on.
>>    Note the interaction type info is now in the file name, and is NOT
>>        included in the .par file (see below).
>>
>> [4] The format of the .par file is now as follows:
>>
>> C4.A-D19.T:A55.ALA 1a73.pdb +     8.6310  -99.8367
>> # identifier, PDB file name, '+' or '-' as defined by dot(dz1, dz2)
>> # followed by "translational distance" and "rotational distance", as in #
>> Pabo, except that "translational distance" is NEGATIVE if it is below # the
>> base-pair mean plane. "rotational distance" is within [-180 to +180]
>>
>>   -3.6380    7.5388    2.1037    0.2592   38.5504  -93.9814
>> # six rigid body parameters: tx, ty, tz, rx, ry, rz
>>
>>    3.6415    7.1395    3.2034  # AA frame origin
>>   -0.1708   -0.8874   -0.4282  # x-axis
>>    0.8903    0.0471   -0.4529  # y-axis
>>    0.4220   -0.4586    0.7821  # z-axis
>> # The above 4 lines define the AA reference frame w.r.t. the bp frame, and
>> # can be *rigorously* deduced from the 6 rigid parameters. They are #
>> redundant, and can be safely ignored. They are included here for info #
>> purpose only.
>>
>>    3.6277    7.1391    3.1907  # CA atom coordinates
>>
>> [5] In processing all the PDB files in batch mode, you need to first run
>>    "snap -c" to initialize all the files. Then each run will "append" to
>>    the corresponding files to get the compilation of the whole set.
>>
« Last Edit: March 01, 2012, 06:01:53 pm by xiangjun »

Offline Ming (Stacey)

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Re: general questions about SNAP- rotation parameters
« Reply #8 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.


Offline xiangjun

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Re: general questions about SNAP- rotation parameters
« Reply #9 on: March 01, 2012, 05:58:43 pm »
Thanks, that's helpful -- not only to your own understanding, but also to those who want to know the details.

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.