Messages

1

RNA structures (DSSR) / Re: 1MZP

« on: August 23, 2016, 04:31:22 pm »

Hi Xiang-Jun,

Thank you for the explanation. It makes sense, if DSSR defines a junction loop by also considering the pseudo knotted pairs then it won't define a k-turn motif since there is no internal loop.

Yes, I am familiar with Lilley's k-junction definition. It is found in TPP riboswitches I guess.
On my side, I am also not considering the k-junctions for now. Thanks a lot!

Sincerely,
Cigdem

2

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.

3

RNA structures (DSSR) / Re: Bending angle of internal loops

« on: July 22, 2016, 01:48:49 pm »

Hi Xiang-Jun,

In that case, if two stems making 130 degree between them will be calculated as having a 50 degree bend angle. Do you consider it as a possible kink-turn? For example look at 2JTP.

Cigdem

4

RNA structures (DSSR) / Re: Bending angle of internal loops

« on: July 21, 2016, 05:01:07 pm »

Hi Xiang-Jun,

Thank you for the explanation. I ran DSSR for a set of RNA structures and checked the bend angles. I see that the bend angle of the internal loops is always less than 90 degrees.

Could you please explain me how exactly do you calculate the bend angle after determining the helical axes? How do you choose the directions?

In my opinion, since the bend angle is the angle between two stems, it should be in 0-180 degrees range.

Best regards,
Cigdem

5

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

6

Feature requests / Re: Internal loops

« on: July 11, 2016, 02:50:44 pm »

Dear Xiang-Jun,

Thank you for your collaboration. It is perfect!

I agree that in the future you may add information about other motifs as well.

No, I didn't know --json option. It will be so helpful. Thank you for letting me know.

Best regards,

Cigdem

7

Feature requests / Re: Internal loops

« on: July 08, 2016, 11:30:37 am »

Hi Xiang-Jun,

This is exactly what I needed! Thank you so much for making things so easier.

Just one more thing, if it is applicable could you please also add kink-turn information at the end of the summary line? So that if the corresponding internal loop has a kink-turn, it will say "kt" maybe?

Thank you again.

Best regards,
Cigdem

8

Feature requests / Re: Internal loops

« on: June 30, 2016, 11:33:00 am »

Hi Xiang-Jun,

That is great! Thanks a lot.

Sincerely,
Cigdem Bayrak

9

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