x3dna_ensemble extract output naming

[chenyuwai]

Dear Dr. Lu,

I am new to 3DNA. I am trying to analyze a MD trajectory created by GROMACS of its base-stacking properties. I have used find_pair to get the base-pair parameters file, then used x3dna_ensemble analyze to produce an output file without much problem. However, after I used x3dna_ensemble extract -a, I got a number of .out files of which I do not know how to use. I assume the files with *_area.out and *_area0.out are the relevant files reporting base-stacking overlap areas, are these not? Which one should I look at? My structure is a single-stranded stem-loop. The stem is picked up by find_pair correctly. And also, what are the various columns in these two .out files?

A second question is if I can do similar thing to "find_pair -s RNA.pdb | analyze" to my MD ensemble using x3dna_ensemble? I hope to be able to do this to look at stacking areas in the non-paired bases in the loop and see their changes over MD time.

Thank you very much for your reply. I am sorry I tried to look at various places including this forum, the 2 papers but could not find the answer.

Wai

[xiangjun]

Hi Wai,

Thanks for using 3DNA!

The different base-stacking areas are related to how the 'polygons' are selected for the overlap calculation. As mentioned in the 2003 3DNA NAR paper, in the Section "Standard stacking diagrams":

The middle frame used in calculating base pair step parameters (Slide, Roll, etc.) is used in 3DNA to reset each dinucleotide in a ‘standard’ orientation (34), which can be transformed into a high quality ‘standardized’ base stacking diagram (Fig. 6). Such diagrams allow for visual inspection of the stacking and hydrogen bonding interactions at the dimer level. A similar image in Figure 3 reveals the twist angle discrepancy in shear‐deformed (base‐mismatched) dinucleotide steps. The stacking interactions are quantified in 3DNA by the shared overlap area, in Ų, of closely associated base rings, i.e. the nine‐membered ring of a purine R (A or G) and the six‐membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. For example, the overlap areas between base rings on the left strands of the dimer steps shown in Figure 6 are 0.63 Ų (C3···G2), 0 Ų (G4···C3) and 1.11 Ų (A5···G4). To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, e.g. the overlap of the amino N4 atom of residue C3 with the five‐membered pyrrole ring of base G2 in Figure 6, an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1′‐O2‐N3‐N4‐C5‐C6‐C1′ atomic sequence. The overlap areas of the bases on the left strand of Figure 6 increase, respectively, to 2.95, 2.66 and 3.94 Ų when these and other exocyclic atoms are included in the calculations. The sum of the intra‐ and interstrand stacking overlaps is provided for each dinucleotide step in the 3DNA output.

So 'area0' corresponds to ring atoms only, and 'area' takes consideration of exocyclic atoms. To make sense of the x3dna_ensemble output, it certainly helps to have a better understanding of how 3DNA works on a single structure.

what are the various columns in these two .out files?

The output is a row-by-col matrix, where 'row' is the number of models, and 'col' is the number of (base-pair) steps. Again, checking a single structure with make it clear.

A second question is if I can do similar thing to "find_pair -s RNA.pdb | analyze" to my MD ensemble using x3dna_ensemble? I hope to be able to do this to look at stacking areas in the non-paired bases in the loop and see their changes over MD time.

Check the --single (-s) option to x3dna_ensemble analyze

Since you are "trying to analyze a MD trajectory created by GROMACS", you may well find "do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations by Kumar and Grubmuller useful. You may also find the DSSR program relevant: it certainly has a better user manual.

Whenever in doubt, do not hesitate to ask. Any 3DNA-related questions are always welcome on the Form.

HTH,

Xiang-Jun

[chenyuwai]

Dear Xiang-Jun,

Thank you for the speedy reply. I have tried single PDB with "analyze", the output .outs file is much easier to understand with all the labels and annotations.  But I haven't tried x3dna_ensemble with single PDB. I'll try that and see if I can understand better. Nice weekend.

Wai