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Author Topic: SCHNArP: Global Parameters  (Read 2715 times)

Offline clarebonk

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SCHNArP: Global Parameters
« on: March 19, 2009, 10:13:43 pm »
I am trying to build an RNA using only global parameters (not CEHS parameters).

So, I run schnarp and first enter #2 for "Use GLOBAL helical parameters."  Then I enter #2 again for "Use a full set of GLOBAL parameters."  The next thing schnarp wants is a Sequence-GLH parameter file name.  The default is "GLH_seq.dat".  I've read both READMEs, looked in the Example directory, and googled, but I am not sure how a Sequence-GLH parameter should be formatted.  Of course, I can look through the function step_GLH in rebuild.c to see how it reads in the file and emulate that, but I was wondering if there was a better source of information.

Also, step_GLH calls function comp_base in cmn_fncs.c to ensure no illegal bases exist.  However, only ATCG are hard coded as valid bases.  Since I'm trying to build RNA, I have Uracils.  Is this function going to cause me problems once I do get a GLH_seq.dat file?  Or, does functionality not exist for building RNA from purely global parameters?

Thanks ahead of time!

Offline xiangjun

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Re: SCHNArP: Global Parameters
« Reply #1 on: March 20, 2009, 10:58:05 pm »
Well, once you try to get into details on how things actually work in SCHNAarP, or any software tools in that matter,  you will surely have lots of questions. Getting the software compiled and run is just the beginning.

Overall, SCHNAarP was produced 10+ year ago, and it is now superseded by 3DNA (v2.0). That does not mean the underlying algorithms are out of date. Just on the contrary, the mathematics is valid and solid, and it forms one of the foundations of 3DNA. Yet by design, the reference frames in CEHS and SCHNAaP only apply to double helical DNA/RNA structures (with Waton-Crick bps). As a special note, stretch for a Watson-Crick base-pair is ~5.4 A instead of 0 A, as would be expected, and from other analysis programs.

Now for your specific questions:

There is no special documentation to the file format on Sequence-GLH parameter file. It would be self-explanatory by following an example. For your case, first enter #2 for "Use GLOBAL helical parameters." Then I enter #1 for "Uniform regular helix" and you will get an output file "GLH_seq.dat". Examine it and post back here what you find. And have a look of 1bna.glh following schnaap.

Building RNA structure from a set of SCHNAaP global parameters would be practically meaningless (see above). With the source code in hand and once you get to the bottom of it, you could borrow the idea to apply to your specific applications. This does take time and efforts -- it is not just about the C code, but more about the underlying mathematics and the nucleic acid structure problems being addressed.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline clarebonk

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Re: SCHNArP: Global Parameters
« Reply #2 on: April 02, 2009, 12:56:59 pm »
I followed your instructions, and found the format of GLH_seq.dat to be something like this for a length two helix:

    2 base-pairs
       X-dsp   Y-dsp    Rise   Incl.    Tip    Twist
A-U     0.30    0.39    0.00   27.52  -24.12    0.00
G-C     0.30    0.39    4.22   27.52  -24.12   31.90

It is the same information as in the *.glh files, removing the first 6 base pair parameters Shear through Open.

I found that selecting (in schnarp) "2. Use GLOBAL helical parameters" then "1. Uniform regular helix" then "5. Other regular double helical structures" is the path that I was looking for, since it prompts for 6 parameters, and I am minimizing the RMSD from the output to my original helix.

I did need to change the Ts to Us in the function comp_base so I wouldn't get the error "Illegal base exists!" and it would find the right file in the folder BaseGeo.  I am getting correct RNA output because I select "RNA" when prompted for "Base geometry set to use (Dft NDB96)."

Everything is working great!

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.