How does rebuild work?

[tanoramb]

Dear Xiang-Jun,

This is a terrific forum! Just one thing is not clear to me in your 3DNA manual, given the conformational parameters (slide, shift, rise, tilt, roll, and twist), did you use a standard base-pair(coordinates for all atoms for a base-pair are given in a standard reference) to build coordinates for a base-pair in an experimental reference?

I got what you said in your manual about building bases (calculating experimental origins and transformation matrices), but how to get pairs is not clear to me, would you please help me on it? Thanks in advance.

Best,
Baoqiang

[xiangjun]

Dear Baoqiang,

Thanks for using 3DNA and welcome to the forum!

In building a DNA (RNA) structure, the "rebuild" program first generates the base-pair structural unit based on bp parameters (propeller, buckle, etc) and then set the bp with reference to the middle bp frame. Have a look of the file "bp_step.par" following "analyze" to check the format (for v1.5, see file $X3DNA/Examples/Analyze_Rebuild/README). If no bp parameters are available, they are assumed to be zeros (see $X3DNA/Examples/Calladine_Drew/p56a.dat for an example).

Once the first bp is set w.r.t. to its middle frame, the step parameters (slide, roll etc) are applied, which defines the position and orientation of the 2nd bp.  As with the 1st bp, the 2nd bp needs to be constructed with corresponding bp parameters and set w.r.t. to its middle frame, This is repeated as many times as needed until the full structure is built. It  follows that the "rebuild" structure is always set w.r.t. the 1st bp reference frame.

For a more detailed description, please refer to the SCHNArP paper: 3DNA uses exactly the same procedure.

HTH,

Xiang-Jun