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91
RNA structures (DSSR) / Re: DSSR multiplets
« Last post by xiangjun on October 08, 2017, 02:07:35 pm »
OK. Now I see what you meant by "aligned".

The algorithm in DSSR for setting the 'planar' view of a multiplet works as follows:

  • The base reference frame of each nucleotide in the multiplet is known. See for example
    x3dna-dssr -i=1ehz.pdb --json | jq .nts[0].frame
  • The z-axis of the multiplet is the mean of the z-axes of all base frames, using the first (z1) as reference. If the z-axis (z2) of the other base is anti-parallel to z1 [i.e., dot(z1, z2) < 0], z2 is reversed before taking the average. The z-axis of the multiplet is then normalized.
  • The x-axis of the multiplet is defined similarly, and corrected for orthogonality with the z-axis.
  • The y-axis is defined as cross(z_axis, x_axis) for a right-handed reference system.
  • The origin of the multiplet is the geometric average of the origins of the base frames.

The multiplet is then transformed to the coordinate frame defined above. By definition, it has the 'top' view to show the planarity of the multiplet. Note that the x-axis and y-axis of the multiplet could be defined differently. They correspond to different rotations around the z-axis in the multiplet plane.

Over the development of DSSR (and 3DNA), I've tried different approaches in setting the x-axis and y-axis of the multiplet. No users have noticed/reported such subtle changes. If you'd like to have full control over the multiplet coordinates, please try the DSSR --frame option (see the DSSR User Manual).

For completeness, DSSR also provides the --raw-xyz that outputs the original coordinates as in the input PDB/mmCIF file, without any further transformations.

HTH,

Xiang-Jun
92
RNA structures (DSSR) / Re: DSSR multiplets
« Last post by febos on October 08, 2017, 12:15:49 pm »
Dr. Lu,

I'm sorry for not being clear. By "aligned" I mean that if I take several base triples from an arbitrary dssr-multiplets.pdb file and look at them in Jmol - they appear aligned. So my question is about processing coordinates of the nucleotides - the coordinates of nucleotides in dssr-multiplets.pdb are different from initial PDB entry. Could you please explain what transformation DSSR performs in there?

Respectfully,
Eugene
93
RNA structures (DSSR) / Re: DSSR multiplets
« Last post by xiangjun on October 08, 2017, 11:54:14 am »
Hi Eugene,

Welcome back! I'm glad to hear of your continued interest in using DSSR in your project(s).

Each multiplet identified by DSSR is outputted in sequential order. The multiplets are ordered by the number of nucleotides, and then by sequential numbers. I do not know if that's what you mean by "aligned". You may find the section "Summary of structural features of ** nucleotides" relevant.

As a side note, (by default) each multiplet has been reoriented in the 'top' view to illustrate the overall planarity of the nucleotides.

HTH,

Xiang-Jun

PS. DSSR contains many undocumented features. The DSSR User Manual is over 90 pages, and that may be already too long for general users.
94
RNA structures (DSSR) / DSSR multiplets
« Last post by febos on October 08, 2017, 10:57:50 am »
Dear Dr. Lu,

At the moment I study RNA base triples found in RNA-containing PDB entries using DSSR. I and my students have created a new classification of base triples with respect to secondary structure environment of their nucleotides and now we are planning to implement the classification within our database's web-interface.
We thought it would be helpful to include the 3D visualization of an arbitrary set of aligned base triples and while working on that problem I've noticed that DSSR stores aligned base triples within its output file named dssr-multiplets.pdb.
Could you please tell me how you align multiplets in DSSR? Unfortunately I couldn't have found this information in DSSR tutorials.

Thanks in advance.

Respectfully,
Eugene
95
Feature requests / Re: Z-steps
« Last post by xiangjun on September 28, 2017, 02:08:06 pm »
Hi Pascal,

I read both of your papers mentioned above, and like the thoroughness of your analyses. 3DNA/DSSR certainly contains features for characterizating Z-steps in DNA/RNA, and I could consolidate them into a more user-friendly form.

For the benefit of other users, and to avoid any potential technical caveats, please provide concrete examples with defining features of Z-steps, presumably based on your publications.

Best regards,

Xiang-Jun
96
Feature requests / Z-steps
« Last post by Auffinger on September 28, 2017, 12:04:38 pm »
Hi Xiang-Jun,

I am not sure since I havent' checked 3DNA pages for a while
if you implemented a feature to detect Z-steps in RNA and DNA systems
as defined in:
(if not, I think it would be nice to have and probably pretty easy to do for you).

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
RNA. 2017 Mar;23(3):259-269. doi: 10.1261/rna.059097.116. Epub 2016 Dec 20.

and

'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
Nucleic Acids Res. 2016 Jul 8;44(12):5944-56. doi: 10.1093/nar/gkw388. Epub 2016 May 5.

Thanks for your reply,

All the best,

Pascal
97
RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« Last post by xiangjun on September 22, 2017, 02:45:09 pm »
I've followed the literature on G-qudraplex structure for a long while, and 3DNA/DSSR already contain basic components for making sense of it. This thread ha prompted me to integrate the pieces, and to add tailored analysis/annontation features for G-quadraplex. The coming DSSR v1.7.0 release will have a section dedicated to G-qudraplex, as it does for the i-motif.

Xiang-Jun
98
RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« Last post by xiangjun on September 20, 2017, 06:31:49 pm »
Quote
Hi, for the structure 2chj, http://www.rcsb.org/pdb/explore/explore.do?structureId=2chj, DSSR produces some odd output.

I understand what you meant. The helix/stem/loop/ss-fragment definitions, as described in the 2015 DSSR paper in NAR, follow the literature on RNA secondary structure which is based on canonical base pairs (WC and G-U wobble). From my experience, the community is not necessarily consistent with its nomenclature/definition (if any), on the basics of (double) helix/stem/arm/paired-region/loop/pseudoknot and coaxial stacking.

Quote
First, it identifies two helices instead of one. This is somewhat understandable since removing two strands would still produce a helical structure, but it would be nice if DSSR could identify higher-order helices automatically. Perhaps the definition of a base-pair could be generalized to include any number of nucleotides, and helices could be defined based on the stacking of these generalized base-pairs.

As you noticed, DSSR identifies two helices from a G-quadruplex structure, which clearly looks odd for this well-known structure type. This is just how DSSR works on general RNA/DNA structures where duplexes are the most frequent. Higher-level structures are case-specific: for example, G-quadruplex and i-motif are all composed of 4 strands, even though they are obviously different.

As of v1.6.1-2016aug22, DSSR already can detect and characterize i-motifs (see the DSSR User Manual). For a G-quadruplex structure (e.g. 2chj), did you notice the section "List of 4 G-quartets" as shown below:

Code: [Select]
List of 4 G-quartets
   1 nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
   2 nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
   3 nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
   4 nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23

Is the above info useful? What more do you need? DSSR can potentially separate the four strands, and characterize the loops and directionality between the strands (as for i-motif).

Quote
Second, it identifies each strand as a single-stranded segment, which is clearly a bug. Not sure how a single-stranded segment is defined, but I'm guessing it has to do with there being no first order base pairs (i.e. one to one base pair) in the structure.

You may call DSSR's list of single-stranded segments as "clearly a bug", from your own perspective for a G-quadruplex structure. Nevertheless, the output of DSSR follows the conventions largely adopted by the RNA (secondary) structure community. To the extent, of course, I understand and can put them into a self-consistent software program.

As I see it, your concerns about DSSR (in general) can be addressed by further its characterizations of G-quadruplex specific features, as it already does for i-motif. No size fits all. DSSR has been designed to work for the most common cases (by default), but can be quickly tailored for specified needs on a case-by-case basis. Browsing the Forum, you'll find several such cases.

HTH,

Xiang-Jun
99
RNA structures (DSSR) / Odd output for G-quadruplex structure
« Last post by jms89 on September 20, 2017, 02:50:41 pm »
Hi, for the structure 2chj, http://www.rcsb.org/pdb/explore/explore.do?structureId=2chj, DSSR produces some odd output.

First, it identifies two helices instead of one. This is somewhat understandable since removing two strands would still produce a helical structure, but it would be nice if DSSR could identify higher-order helices automatically. Perhaps the definition of a base-pair could be generalized to include any number of nucleotides, and helices could be defined based on the stacking of these generalized base-pairs.

Second, it identifies each strand as a single-stranded segment, which is clearly a bug. Not sure how a single-stranded segment is defined, but I'm guessing it has to do with there being no first order base pairs (i.e. one to one base pair) in the structure.

100
MD simulations / Re: How to analyze helical parameters of DNA with unnatural bases
« Last post by xiangjun on September 18, 2017, 10:38:50 pm »
Hi Xiehuang,

I've had a look of your attached PDB files. DX/DY/DZ deviate too much from normal purines in terms of base orientation and atoms nomenclature, as shown in the attached image for DX. They are no longer recognized as nucleotides so "find_pair" cannot identify any pairs associated with them. This is clearly a limitation of 3DNA.

Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.