Proposed changes in DSSR v1.2

[xiangjun]

The coming release of DSSR v1.2.0 includes proposed format changes in existing sections and a newly added section, as detailed below. I'd like to keep the community informed and hopefully to hear your comments before the 'official' release. To have a look of new features, try the web-interface to DSSR.

Non-pairing interactions (option --non-pair)
Currently, the format is like this, using 1msy as an example:

Code: [Select]

List of 30 non-pairing interactions
      nt1              nt2              base-stacking    H-bonding
   1 A.U2647          A.G2648             1.0(0.5)
   2 A.G2648          A.C2649             7.3(4.6)
   8 A.C2652          A.G2669             0.2(0.0)
   9 A.U2653          A.A2654             3.3(2.0)    H-bonds[1]: "OP2-O2'(hydroxyl)[2.62]"
  12 A.G2655          A.A2665             0.0(0.0)    H-bonds[3]: "N1(imino)-OP2[2.77],N2(amino)-OP2[3.34],N2(amino)-O5'[2.89]"
The corresponding section in v1.2.0 is:

Code: [Select]

List of 30 non-pairing interactions
   1 A.U2647        A.G2648        stacking: 1.0(0.5)--pm(>>,forward)
   2 A.G2648        A.C2649        stacking: 7.3(4.6)--pm(>>,forward)
   8 A.C2652        A.G2669        stacking: 0.2(0.0)--mm(<>,outward)
   9 A.U2653        A.A2654        stacking: 3.3(2.0)--pp(><,inward) H-bonds[1]: "OP2-O2'(hydroxyl)[2.62]"
  12 A.G2655        A.A2665        H-bonds[3]: "N1(imino)-OP2[2.77],N2(amino)-OP2[3.34],N2(amino)-O5'[2.89]"
The header line is removed. For each pair of nucleotides involved in non-pairing interactions, the stacking or H-bonding part is listed only if it is present. For example, #1 in the list, A.U2647 vs. A.G2648, has only stacking interaction, no H-bonding; #12 (A.G2655 vs. A.A2665) has only H-bonding interactions, no base-stacking; #9 (A.U2653 vs. A.A2654) has both base-stacking and H-bonding interactions.

I've also introduced a classification of base-stacking interactions, into 4 categories, depending on the relative orientations of base faces, defined by the standard base reference frame: pm, mp, pp, and mm. Here 'p' is for plus, meaning the other base is on the +z-axis side of the referenced base; 'm' for minus, meaning the other base is on the –z-axis side of the referenced base. The corresponding symbols used by Major et al are put in parentheses; pm(>>, forward), mp(<<, backward), pp(><, inward), and mm(<>,  outward). Note that I prefer to call pm(>>) forward instead of upward, and mp(<<) backward instead of downward.

List of isolated canonical pairs
An extra column is added at the beginning to specify the helix that the isolated WC/wobble pair is part of. If it does not belong to any helix, the symbol n/a is used. Using 1msy as an example, the new output for this section would be as below.

List of 1 isolated WC/wobble pair
  Note: isolated WC/wobble pairs are assigned negative indices to
        differentiate them from the stem numbers, which are positive.
        --------------------------------------------------------------------
[#1]   -1 A.C2658        A.G2663        C-G WC           19-XIX    cWW  cW-W

Phosphate interactions (option --po4)
In addition to H-bonding and capping interactions, coordinations with metal ions will be reported. To keep things simple, the OP1-hbonds or OP2-hbonds listing also includes corresponding metals that the non-bridging oxygen coordinates with. Using the yeast phenylalanine 1ehz as an example, the new output looks like below:

Code: [Select]

List of 18 phosphate interactions
   1 A.U7            OP1-hbonds[1]: "MG@A.MG580[2.60]"
   ...........
   6 A.G19           OP1-hbonds[2]: "N4@A.C60[3.27],MN@A.MN530[2.19]"
   ...........
The new option --idstr to replace --long-idstr
The specific --long-idstr option has been replaced by --idstr, which can take value long (i.e., --idstr=long) to achieve previous functionality. Moreover, it can take short (i.e., --idstr=short) as an argument to list only name and number of nucleotides (e.g., A21).

Xiang-Jun