Topics

1

RNA structures (DSSR) / 1MZP

« on: August 23, 2016, 02:38:21 pm »

Hi Xiang-Jun,

I was looking at the structure 1MZP and I noticed that DSSR does not notify its k-turn motif. However, if I use --nested option, it gives the k-turn information.
I noticed that it is considered as having 1 internal loop (with 1 1 unpaired bases) and a 6-way junction. When I look at the 2D structure, I see two internal loops and a pseudoknot. This is a little confusing for me.

2

RNA structures (DSSR) / Bending angle of internal loops

« on: July 12, 2016, 11:06:11 am »

Hi Xiang-Jun,

When I use json option, I see that you also calculate bending angle.

For 1e7k:

"bending_angle": 66.74

Since I am also interested in bending (and torsion) angles, could you please give me details on how you calculate the bending angle of internal loops? I wasn't able to find information on that.

Thank you.
Cigdem

3

Feature requests / Internal loops

« on: June 29, 2016, 02:52:33 pm »

Hi Xiang-Jun,

I need to gather some information on internal loops and I believe DSSR would be a great tool for this purpose.
What I need is for example for 1E7K:

1) Length of the unpaired regions as you give in internal loops section:

****************************************************************************

List of 2 internal loops

   1 asymmetric internal loop: nts=11; [5,2]; linked by [#1,#2]

     nts=11 CAAUGAGCGAG C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.C42,C.G43,C.A44,C.G45

       nts=5 AAUGA C.A29,C.A30,C.U31,C.G32,C.A33

       nts=2 GA C.G43,C.A44

2) Nucleotide numbers of first and last pairs of the helices as you give in the kink turns section (but I need this info for non kink-turns, too):

****************************************************************************

List of 2 possible kink turns

   1 Normal k-turn with GA on helix#1 (same as C- and NC-helix); iloop#1

      C#1[CG C.C28,C.G45] [GA C.G32,C.A44] NC#2[CG C.C42,C.G34]

      strand1 nts=10; GCCAAUGAGG C.G26,C.C27,C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.G35

      strand2 nts=7; CCGAGGC C.C41,C.C42,C.G43,C.A44,C.G45,C.G46,C.C47


3) Length of the helices as you give in the stems section:


****************************************************************************

List of 4 stems

  Note: a stem is defined as a helix consisting of only canonical WC/wobble

        pairs, with a continuous backbone.

      stem#number[#helix-number containing this stem]

      Other terms are defined as in the above Helix section.

      --------------------------------------------------------------------

  stem#1[#1] bps=3

      strand-1 5'-GCC-3'

       bp-type    |||

      strand-2 3'-CGG-5'

      helix-form  AA

   1 C.G26          C.C47          G-C WC           19-XIX    cWW  cW-W

   2 C.C27          C.G46          C-G WC           19-XIX    cWW  cW-W

   3 C.C28          C.G45          C-G WC           19-XIX    cWW  cW-W

  --------------------------------------------------------------------------

  stem#2[#1] bps=2

      strand-1 5'-GG-3'

       bp-type    ||

      strand-2 3'-CC-5'

      helix-form  .

   1 C.G34          C.C42          G-C WC           19-XIX    cWW  cW-W

   2 C.G35          C.C41          G-C WC           19-XIX    cWW  cW-W

  --------------------------------------------------------------------------

So, for 1E7K the information would be like:

1E7K C 5 2 28 45 42 34 3 2

I need this information also for other internal loops that don't have a kink-turn. Do you think it is applicable?
Thanks a lot.

Cigdem Bayrak