irregular structure

[bala]

I want to calculate the struc.parameters for a irregular structure. The structure contains mismatche and bulge region.  We want to calculate  all parameters especially for these two regions but when i tried in 3DNA, it calculates parameters only for those pairs it for which it detects HYD bond.  I dnt know how to get aroud of this problem. Can anyone pls share your experience of using 3DNA for structures which are having bulges and folds etc.

I have uploaded the structure in the link provided the announcement section of 3DNA forum. The structure name is "structur.pdb".

thanks
Bala

[xiangjun]

I do not think that I am in a position to provide any concrete suggestion on how to analyze the irregular nucleic acid structures from your MD simulation. Nevertheless, it would seem to push 3DNA (or any analyzing tool for that matter) too much trying to calculate base-pair parameters for a flipping out base or step parameters for a non-double helical region.

You could, however, calculate all the backbone and chi torsion angles, and sugar conformational parameters (with find_pair -s option). You can also generate a blocview image (blocview -d my.pdb) and display the block image with PyMOL (pymol t.r3d).

As with any software tool, the issue is not just about   calculating some numbers, but more importantly on understanding what the numbers really mean.

HTH,

Xiang-Jun