Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Messages - xiangjun

Pages: 1 2 [3] 4 5 ... 78
31
Quote
list all the hydrogen bond between RNA and ligand?

Do you have a concrete example of such listing?

Xiang-Jun

32
Feature requests / Re: Rebuild DNA structures based on 28 parameters
« on: October 28, 2017, 07:03:37 pm »
Dear Akhilesh Mishra,

No, you cannot build DNA structures based on the 28 listed parameters simultaneously. At least in my understanding, they are not fully independent.

The 3DNA rebuild program can rigorously reconstruct the base-pair geometry using either of two sets of 12 parameters: 6 base-pair parameters (propeller, buckle, etc.) + 6 step parameters (roll, slide, etc.), or 6 base-pair parameters (propeller, buckle, etc.) + 6 helical parameters (x-displacement, inclination, etc.). The 2003 3DNA NAR paper provides details on the relationship between the step and helical parameters, in the section "Dimer step parameters". Fig. 4 and Table 1 taken from the 2003 3DNA NAR paper are shown below, for completeness.






So the answer is no, this feature request cannot be fulfilled.

Xiang-Jun

33
RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« on: October 20, 2017, 01:22:48 pm »
As a followup, it is worth noting that DSSR v1.7.0-2017oct19, released yesterday, contains features to automatically identify and fully characterize G-quadruplexes. Here are some examples:

  • PDB entry: 2chj
    List of 1 G4-stem
      stem#1[#1] layers=4 inter-molecular parallel
       1 syn=---- WC-->Major area=23.67 rise=3.04 twist=21.10 nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
       2 syn=---- WC-->Major area=9.60  rise=3.65 twist=32.28 nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
       3 syn=---- WC-->Major area=18.59 rise=3.68 twist=22.74 nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
       4 syn=---- WC-->Major                                  nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
        strand#1  +1 DNA syn=---- nts=4 GgGg A.DG2,A.LCG3,A.DG4,A.LCG5
        strand#2  +1 DNA syn=---- nts=4 GgGg B.DG8,B.LCG9,B.DG10,B.LCG11
        strand#3  +1 DNA syn=---- nts=4 GgGg C.DG14,C.LCG15,C.DG16,C.LCG17
        strand#4  +1 DNA syn=---- nts=4 GgGg D.DG20,D.LCG21,D.DG22,D.LCG23
  • PDB entry: 5dww
      stem#1[#1] layers=3 INTRA-molecular parallel
       1 syn=---- WC-->Major area=11.63 rise=3.65 twist=31.14 nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG14
       2 syn=.--- WC-->Major area=10.64 rise=3.54 twist=28.10 nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG15
       3 syn=---- WC-->Major                                  nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG16
        strand#1  +1 DNA syn=-.- nts=3 GGG A.DG1,A.DG2,A.DG3
        strand#2  +1 DNA syn=--- nts=3 GGG A.DG5,A.DG6,A.DG7
        strand#3  +1 DNA syn=--- nts=3 GGG A.DG9,A.DG10,A.DG11
        strand#4  +1 DNA syn=--- nts=3 GGG A.DG14,A.DG15,A.DG16
        loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
        loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT8
        loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT12,A.DT13
  • PDB entry: 2hy9
      stem#1[#1] layers=3 INTRA-molecular anti-parallel
       1 syn=ss-s Major-->WC area=13.69 rise=3.14 twist=19.08 nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22
       2 syn=--s- WC-->Major area=13.40 rise=3.05 twist=28.05 nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
       3 syn=--s- WC-->Major                                  nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24
        strand#1  +1 DNA syn=s-- nts=3 GGG 1.DG4,1.DG5,1.DG6
        strand#2  +1 DNA syn=s-- nts=3 GGG 1.DG10,1.DG11,1.DG12
        strand#3  -1 DNA syn=-ss nts=3 GGG 1.DG18,1.DG17,1.DG16
        strand#4  +1 DNA syn=s-- nts=3 GGG 1.DG22,1.DG23,1.DG24
        loop#1 type=propeller strands=[#1,#2] nts=3 TTA 1.DT7,1.DT8,1.DA9
        loop#2 type=lateral   strands=[#2,#3] nts=3 TTA 1.DT13,1.DT14,1.DA15
        loop#3 type=lateral   strands=[#3,#4] nts=3 TTA 1.DT19,1.DT20,1.DA21
  • PDB entry: 5hix
      stem#1[#1] layers=4 inter-molecular anti-parallel
       1 syn=s--s Major-->WC area=12.93 rise=3.64 twist=16.82 nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
       2 syn=-ss- WC-->Major area=18.96 rise=3.71 twist=35.87 nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
       3 syn=s--s Major-->WC area=15.16 rise=3.64 twist=18.64 nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
       4 syn=-ss- WC-->Major                                  nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
        strand#1  +1 DNA syn=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
        strand#2  -1 DNA syn=-s-s nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
        strand#3  -1 DNA syn=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
        strand#4  +1 DNA syn=s-s- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12
        loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
        loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT5,B.DT6,B.DT7,B.DT8
  • PDB entry: 2m4p
      stem#1[#1] layers=3 INTRA-molecular parallel bulged-strands=1
       1 syn=---- WC-->Major area=8.38  rise=3.64 twist=33.34 nts=4 GGGG A.DG3,A.DG8,A.DG12,A.DG16
       2 syn=---- WC-->Major area=10.73 rise=3.23 twist=32.42 nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
       3 syn=---- WC-->Major                                  nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
        strand#1* +1 DNA syn=--- nts=3 GGG A.DG3,A.DG5,A.DG6 bulged-nts=1 T A.DT4
        strand#2  +1 DNA syn=--- nts=3 GGG A.DG8,A.DG9,A.DG10
        strand#3  +1 DNA syn=--- nts=3 GGG A.DG12,A.DG13,A.DG14
        strand#4  +1 DNA syn=--- nts=3 GGG A.DG16,A.DG17,A.DG18
        loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
        loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11
        loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT15

Other featured are also available, but not currently reported (as shown above). Details on the underlying algorithms and a survey of PDB entries will be reported in a formal publication.

Best regards,

Xiang-Jun

34
RNA structures (DSSR) / Re: FRABASE
« on: October 18, 2017, 01:00:29 pm »
Hi Honglue,

Please see the FAQ entry "How does DSSR compare with other tools?" in the DSSR User Manual for my thought on such comparisons.

In addition to the above general response, below is a quote from "RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures":

Quote
Several dedicated programs, web-accessible servers and databases have been proposed for processing and analysis of the PDB files (c.f. [3]) to study three-dimensional RNA structure. Among them, two particular programs are of general use and of specific importance to our work: 3DNA [4] and RNAView [5]. The first program calculates a complete set of rigid-body parameters that describe the detailed geometry of double helices extracted from the tertiary RNA structures. The second one finds all base pairs and multiplets in the RNA structure and offers the classification of canonical and non-canonical base-pairs. Both programs have been implemented in web-servers [2, 6].

In the current context, it is safe to say: DSSR = 3DNA + RNAview + ...

Xiang-Jun

35
General discussions (Q&As) / Re: How to install 3DNA on Windows 8
« on: October 15, 2017, 11:54:37 am »
Did the FAQ entry “How to set up 3DNA on Windows” help?

Xiang-Jun

36
RNA structures (DSSR) / Re: DSSR multiplets
« 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

37
RNA structures (DSSR) / Re: DSSR multiplets
« 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.

38
Feature requests / Re: Z-steps
« 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

39
RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« 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

40
RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« 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

41
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

42
RNA structures (DSSR) / Re: Definition of Helix Form
« on: September 15, 2017, 11:27:50 pm »
Hi Honglue,

Thanks for your continued interest in DSSR's classifications of A-, B- and Z-helical forms. There are actually many such details in DSSR which I take as 'experimental' and are not published in the 2015 NAR paper or documented in the user manual.  Some of them will certainly end up in new publications, but no timelines.

As for DSSR reported helical forms, do they make sense? Or did you notice anything peculiar? I'd welcome your feedback.

Xiang-Jun

PS. I attended your advisor seminar (very informative) early this month at Rutgers. I saw your name in his acknowledgment list...

43
RNA structures (DSSR) / Re: Groove width distance in DSSR
« on: September 15, 2017, 08:43:33 pm »
Quote
I just want to kindly make sure that the output groove_widths in the json file should be [minor_groove_width, minor_groove_width_refined, major_groove_width, major_groove_width_refined], not [minor_groove_width, major_groove_width,, minor_groove_width_refined, major_groove_width_refined], right?

You're right. The four numbers are minor groove width (raw and refined) and major groove width (raw and refined), as in the listing of 3DNA analyze output.

Xiang-Jun

44
General discussions (Q&As) / Re: Single Stranded DNA
« on: September 14, 2017, 12:46:58 pm »
Quote
is there a software suitable for single stranded DNA structure modelling

This is a vague question, and I'm not sure how to answer it. Did you know the NAB tool from the David Case laboratory at Rutgers? NAB is a flexible "molecular manipulation language" designed for the "Generation of Models for 'Unusual' DNA and RNA". In principle, NAB in combination with AMBER should do the trick.

As far as 3DNA/DSSR goes, the "fiber" program can generate arbitrary linear double or single-stranded DNA models. The other two programs, "rebuild" and "mutate_bases", can also be applied to certain aspects of modeling studies (see my blogpost "The 3DNA mutate_bases program is cited in Nature").

Quote
... Could that be a workable solution?

What you said make sense, in general. However, only doing it will reveal concrete caveats and possible solutions. Please post back if you think 3DNA/DSSR may be of some help along the way, and I'll try my best to help.

As a side note, you may already know "RNA-Puzzles", and the numerous tools available for RNA modeling.

Best regards,

Xiang-Jun

 

45
General discussions (Q&As) / Re: construct dna hairpin structure
« on: September 05, 2017, 12:02:16 pm »
Thanks for your follow-up.

3DNA should be of help in modifying an RNA structure into its DNA variant. There are several possibilities here. Please use a concrete example to illustrate what you want to achieve.

Xiang-Jun

Pages: 1 2 [3] 4 5 ... 78

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.