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Messages - xiangjun

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1
JoVE / Re: Jove Questions and Supplimental Files
« on: Yesterday at 10:06:14 am »
Hi,

Thanks for your interest in our 2013 3DNA JoVE article. As you noticed, this JoVE section is not complete (unfortunately). Moreover, Andrew Colasanti is no longer involved in the 3DNA project for many years. You may ask Dr. Wilma Olson directly to see if she has the original data files.

Even though I do not have the supplementary files for protocol 4 you requested, you could find an example of the list file by performing the following steps in the $X3DNA/examples/ensemble/md folder. Check the content of file pdb_list.dat.

Code: [Select]
more README
x3dna_ensemble analyze -h
x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble_example3.out
more pdb_list.dat

Best regards,

Xiang-Jun




2
Hi Adolfo,

As mentioned in my initial response, 3DNA/DSSR (and the 3DNA 2.0 web server) does not have the means to convert a coarse-gained (CG) model to an full-atomic 3D structure: 3DNA/DSSR requires base atoms to deduce base types and pairs etc. Maybe it was not that clear, I was suggesting that you check somewhere else for such a utility. Presumably, the resources that produce the CG model should have such options.

A quick Google search led to "Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes". However, it reconstructs atomic details of DNA structures from a three-site per nucleotide CG model. Nevertheless, searching along the line, I'm almost certain there must be an already existing approach that convert P-only CG models to full-atomic models.

Also, posting this question to the CG-modeling community is more likely to get a concrete answer.

Best regards,

Xiang-Jun

3
Hi Adolfo,

Thanks for joining the 3DNA/DSSR user community, and for posting your question on the Forum.

Quote
will it be possible get global helical parameters (e.g. mino/major groove, pitch, rise,..) for a coarse grained double-helix DNA structure using only the P atoms for each residue?

The answer is no. 3DNA/DSSR requires base atoms to deduce base types and pairs etc. Please check for a utility that converts P-only coarse-grained models to full atomic models. It helps if you could share your findings for the community.

Best regards,

Xiang-Jun

5
RNA structures (DSSR) / Re: How to detect very distorted base pair?
« on: January 20, 2020, 06:55:51 pm »
Running DSSR with the default settings on distorted_bp.pdb

Code: [Select]
x3dna-dssr -i=distorted_bp.pdb --more
I got the following:

Code: [Select]
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 K.DOC13        M.DG6          c-G --          n/a       cWW  cW-W
       [-122.8(anti) .... lambda=75.4] [-98.1(anti) .... lambda=84.4]
       d(C1'-C1')=7.91 d(N1-N9)=7.43 d(C6-C8)=9.40 tor(C1'-N1-N9-C1')=-11.8
       H-bonds[1]: "N4(amino)*N1(imino)[3.56]"
       interBase-angle=11  Simple-bpParams: Shear=-0.50 Stretch=0.34 Buckle=0.5 Propeller=-11.4
       bp-pars: [-0.52   0.30    0.26    1.33    -11.32  51.91]

Isn't that what you're looking for?

Xiang-Jun


6
Thanks for your feedback, and for sharing your code with the community. Yes, JSON is the preferred means to connect 3DNA/DSSR to the outside world. 

Best regards,

Xiang-Jun


PS. As a side note, DSSR also has the option --torsion-file (undocumented) which outputs commonly used backbone parameters, including pseudo-torsions you referred to. It serves as the replacement of "analyze -t", and may be useful for quick visual examinations of the output. Here is the DSSR command and output for PDB id 355d (the classic B-DNA dodecamer).

x3dna-dssr -i=355d.pdb --torsion-file -o=355d-tor.txt

Code: [Select]
         Output of DNA/RNA backbone conformational parameters
             DSSR v1.9.8-2019oct16 by xiangjun@x3dna.org
******************************************************************************************
Main chain conformational parameters:

  alpha:   O3'(i-1)-P-O5'-C5'
  beta:    P-O5'-C5'-C4'
  gamma:   O5'-C5'-C4'-C3'
  delta:   C5'-C4'-C3'-O3'
  epsilon: C4'-C3'-O3'-P(i+1)
  zeta:    C3'-O3'-P(i+1)-O5'(i+1)
  e-z:     epsilon-zeta (BI/BII backbone classification)

  chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
    Range [170, -50(310)] is assigned to anti, and [50, 90] to syn

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: ~C2'-endo for C2'-endo like conformation, or
               ~C3'-endo for C3'-endo like conformation
              Note the ONE column offset (for easy visual distinction)

ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
      (P) expressed in the standard reference frame of the 5' base; the value is
      POSITIVE when P lies on the +z-axis side (base in anti conformation);
      NEGATIVE if P is on the -z-axis side (base in syn conformation)
  Dp: perpendicular distance of the 3' P atom to the glycosidic bond
      [Ref: Chen et al. (2010): "MolProbity: all-atom structure
            validation for macromolecular crystallography."
            Acta Crystallogr D Biol Crystallogr, 66(1):12-21]
splay: angle between the bridging P to the two base-origins of a dinucleotide.

          nt               alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type    ssZp     Dp    splay
 1     C A.DC1               ---     ---   -70.0   144.7  -171.8   -98.4    -73(BI)   -105.9(anti)   163.5(C2'-endo) ~C2'-endo     1.60    1.87   20.42
 2     G A.DG2             -69.8  -172.2    43.0   148.1  -151.3  -157.0      6(..)    -85.4(anti)   160.0(C2'-endo) ~C2'-endo     1.46    1.59   21.98
 3     C A.DC3             -39.4   130.5    50.1    93.3  -165.4   -81.2    -84(BI)   -132.4(anti)    65.3(C4'-exo)     ....       2.36    3.05   17.11
 4     G A.DG4             -64.8   174.4    50.1   145.0  -167.3  -144.6    -23(..)    -93.7(anti)   156.2(C2'-endo) ~C2'-endo     2.19    2.01   20.93
 5     A A.DA5             -47.1   156.2    53.7   133.0  -177.5   -90.7    -87(BI)   -118.6(anti)   158.0(C2'-endo) ~C2'-endo     1.92    2.02   19.68
 6     A A.DA6             -64.2  -173.0    46.3   128.0   176.9   -95.8    -87(BI)   -109.2(anti)   152.6(C2'-endo) ~C2'-endo     1.87    2.02   18.84
 7     T A.DT7             -49.0   172.9    48.6   112.7  -176.6   -95.6    -81(BI)   -119.6(anti)   125.2(C1'-exo)  ~C2'-endo     2.03    2.27   18.01
 8     T A.DT8             -54.1   168.3    53.4   114.0   171.5   -95.0    -94(BI)   -119.9(anti)   126.9(C1'-exo)  ~C2'-endo     2.09    2.31   20.88
 9     C A.DC9             -53.3  -173.2    50.8   138.3  -155.9   -96.3    -60(BI)   -112.3(anti)   157.9(C2'-endo) ~C2'-endo     1.17    1.63   19.40
 10    G A.DG10            -60.3   163.2    39.5   143.2  -100.0   146.3    114(BII)   -83.6(anti)   145.6(C2'-endo) ~C2'-endo     1.41    1.25   21.62
 11    C A.DC11            -73.1   144.3    50.8   143.5  -164.4  -126.1    -38(BI)   -112.8(anti)   163.8(C2'-endo) ~C2'-endo     1.11    1.67   19.40
 12    G A.DG12             52.9   144.1   -65.6   147.9     ---     ---     ---       -79.3(anti)   207.4(C3'-exo)     ....        ---     ---     ---

 1     C B.DC13              ---     ---    58.5   138.1  -169.0  -104.8    -64(BI)   -106.9(anti)   163.5(C2'-endo) ~C2'-endo     1.67    1.97   18.36
 2     G B.DG14            -58.3   166.6    49.5   115.0   178.2   -94.3    -88(BI)   -110.2(anti)   129.6(C1'-exo)  ~C2'-endo     2.27    2.38   21.74
 3     C B.DC15            -56.8   160.1    56.8    82.1  -174.4   -84.7    -90(BI)   -137.2(anti)    42.0(C4'-exo)   ~C3'-endo    3.17    3.82   18.25
 4     G B.DG16            -61.6   175.5    62.1   140.9   150.8   -89.6   -120(BI)   -101.7(anti)   168.8(C2'-endo) ~C2'-endo     2.20    2.01   22.29
 5     A B.DA17            -56.3  -160.2    54.1   145.8  -178.3   -91.9    -86(BI)   -108.3(anti)   173.3(C2'-endo) ~C2'-endo     1.36    1.79   18.87
 6     A B.DA18            -61.5   175.7    45.3   113.1   166.4   -91.2   -102(BI)   -112.4(anti)   127.5(C1'-exo)  ~C2'-endo     2.20    2.33   18.64
 7     T B.DT19            -49.1   178.5    51.6   127.6  -172.8  -106.8    -66(BI)   -115.9(anti)   143.0(C1'-exo)  ~C2'-endo     1.86    2.11   19.09
 8     T B.DT20            -44.5   171.8    43.4   135.3  -164.1  -106.8    -57(BI)   -110.1(anti)   151.4(C2'-endo) ~C2'-endo     1.45    1.84   19.32
 9     C B.DC21            -58.1   159.5    51.3    95.5  -170.1   -81.3    -89(BI)   -124.4(anti)    93.3(O4'-endo)    ....       1.97    2.48   17.95
 10    G B.DG22            -67.1   177.0    45.3   143.5  -148.6  -173.0     24(..)    -86.2(anti)   151.2(C2'-endo) ~C2'-endo     1.96    1.90   23.90
 11    C B.DC23            -57.2   129.7    51.4    83.8  -161.3   -77.6    -84(BI)   -150.3(anti)    17.5(C3'-endo)  ~C3'-endo    3.83    4.34   18.70
 12    G B.DG24            -62.1   169.8    52.8    87.7     ---     ---     ---      -141.3(anti)    13.7(C3'-endo)  ~C3'-endo     ---     ---     ---

******************************************************************************************
Virtual eta/theta torsion angles:

  eta:    C4'(i-1)-P(i)-C4'(i)-P(i+1)
  theta:  P(i)-C4'(i)-P(i+1)-C4'(i+1)
    [Ref: Olson (1980): "Configurational statistics of polynucleotide chains.
          An updated virtual bond model to treat effects of base stacking."
          Macromolecules, 13(3):721-728]

  eta':   C1'(i-1)-P(i)-C1'(i)-P(i+1)
  theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)
    [Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews
          of Biophysics, 44(4):433-466]

  eta":   base(i-1)-P(i)-base(i)-P(i+1)
  theta": P(i)-base(i)-P(i+1)-base(i+1)

          nt                eta   theta     eta'  theta'    eta"  theta"
 1     C A.DC1               ---     ---     ---     ---     ---     ---
 2     G A.DG2             165.5  -161.7  -165.6  -177.4  -126.7  -112.3
 3     C A.DC3             179.5  -145.2  -171.9  -147.9  -105.8  -123.9
 4     G A.DG4             158.9  -162.8  -164.8  -179.1  -135.8  -131.6
 5     A A.DA5             174.5  -128.4  -163.1  -149.5  -114.7  -104.0
 6     A A.DA6             168.1  -148.3  -165.5  -160.7  -112.5  -121.4
 7     T A.DT7             179.3  -155.6  -162.3  -163.0  -119.1  -121.9
 8     T A.DT8             172.1  -161.9  -165.4  -168.5  -120.3  -121.7
 9     C A.DC9            -173.0  -123.0  -152.9  -132.0  -106.6   -93.2
 10    G A.DG10            174.2   158.6  -153.5   154.1  -115.5  -152.3
 11    C A.DC11            174.4  -105.9  -158.7  -137.8  -113.5  -106.3
 12    G A.DG12              ---     ---     ---     ---     ---     ---

 1     C B.DC13              ---     ---     ---     ---     ---     ---
 2     G B.DG14            166.8  -152.9  -169.8  -166.3  -123.0  -106.1
 3     C B.DC15            174.1  -170.1  -172.6  -164.6  -104.0  -144.2
 4     G B.DG16            155.8  -134.3  -157.9  -167.2  -135.1  -111.4
 5     A B.DA17           -177.5  -121.1  -153.7  -142.5   -94.4  -102.8
 6     A B.DA18            164.2  -162.9  -170.6  -170.2  -122.5  -128.1
 7     T B.DT19           -178.9  -149.1  -158.1  -158.7  -114.1  -116.5
 8     T B.DT20            177.8  -138.9  -158.3  -153.9  -113.9  -104.5
 9     C B.DC21            173.0  -152.9  -171.8  -151.0  -118.0  -122.5
 10    G B.DG22            163.1   173.9  -167.2   156.7  -137.5  -141.3
 11    C B.DC23            167.8  -144.6   169.4  -150.8  -124.1  -124.9
 12    G B.DG24              ---     ---     ---     ---     ---     ---

******************************************************************************************
Sugar conformational parameters:

  v0: C4'-O4'-C1'-C2'
  v1: O4'-C1'-C2'-C3'
  v2: C1'-C2'-C3'-C4'
  v3: C2'-C3'-C4'-O4'
  v4: C3'-C4'-O4'-C1'

  tm: the amplitude of pucker
  P:  the phase angle of pseudorotation
    [Ref: Altona & Sundaralingam (1972): "Conformational analysis
          of the sugar ring in nucleosides and nucleotides. A new
          description using the concept of pseudorotation."
          J Am Chem Soc, 94(23):8205-8212]

          nt                 v0      v1      v2      v3      v4      tm      P   Puckering
 1     C A.DC1             -20.3    33.1   -33.1    22.1    -1.2    34.5   163.5  C2'-endo
 2     G A.DG2             -23.9    36.6   -34.9    22.3     0.8    37.1   160.0  C2'-endo
 3     C A.DC3             -24.8     5.6    13.9   -28.7    33.8    33.3    65.3   C4'-exo
 4     G A.DG4             -25.7    37.1   -33.9    20.1     3.4    37.1   156.2  C2'-endo
 5     A A.DA5             -20.9    31.2   -29.3    17.7     2.0    31.6   158.0  C2'-endo
 6     A A.DA6             -22.6    30.8   -27.2    14.8     4.8    30.6   152.6  C2'-endo
 7     T A.DT7             -34.2    33.1   -20.1     0.8    20.9    34.8   125.2   C1'-exo
 8     T A.DT8             -35.8    35.4   -22.0     1.8    21.1    36.7   126.9   C1'-exo
 9     C A.DC9             -21.5    31.7   -29.8    18.0     2.0    32.2   157.9  C2'-endo
 10    G A.DG10            -36.1    45.1   -36.0    16.8    11.4    43.6   145.6  C2'-endo
 11    C A.DC11            -21.3    35.1   -35.2    23.4    -1.5    36.6   163.8  C2'-endo
 12    G A.DG12              4.1    12.3   -22.5    25.4   -18.8    25.4   207.4   C3'-exo

 1     C B.DC13            -18.0    29.3   -29.4    19.4    -1.0    30.7   163.5  C2'-endo
 2     G B.DG14            -31.7    32.2   -21.1     3.2    17.9    33.1   129.6   C1'-exo
 3     C B.DC15            -15.4    -9.0    28.1   -37.8    33.6    37.8    42.0   C4'-exo
 4     G B.DG16            -15.6    28.7   -30.2    21.8    -4.0    30.8   168.8  C2'-endo
 5     A B.DA17            -13.5    27.8   -31.1    23.6    -6.5    31.4   173.3  C2'-endo
 6     A B.DA18            -31.3    31.1   -19.7     1.9    18.6    32.4   127.5   C1'-exo
 7     T B.DT19            -28.9    34.5   -27.4    11.1    11.1    34.2   143.0   C1'-exo
 8     T B.DT20            -28.0    37.2   -32.5    17.2     6.6    37.1   151.4  C2'-endo
 9     C B.DC21            -40.0    25.4    -2.4   -21.1    38.2    40.6    93.3  O4'-endo
 10    G B.DG22            -30.7    41.1   -35.3    19.0     6.9    40.3   151.2  C2'-endo
 11    C B.DC23              0.6   -22.5    34.5   -35.1    21.6    36.2    17.5  C3'-endo
 12    G B.DG24              2.9   -23.2    33.3   -32.7    18.6    34.3    13.7  C3'-endo

******************************************************************************************
Assignment of sugar-phosphate backbone suites

  bin: name of the 12 bins based on [delta(i-1), delta, gamma], where
       delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2
       (for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche-
       conformations, respectively) (2x2x3=12 combinations: 33p, 33t,
       ... 22m); 'inc' refers to incomplete cases (i.e., with missing
       torsions), and 'trig' to triages (i.e., with torsion angle
       outliers)
  cluster: 2-char suite name, for one of 53 reported clusters (46
           certain and 7 wannabes), '__' for incomplete cases, and
           '!!' for outliers
  suiteness: measure of conformer-match quality (low to high in range 0 to 1)

    [Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle
          conformers and modular string nomenclature (an RNA Ontology
          Consortium contribution)." RNA, 14(3):465-481]

          nt             bin    cluster   suiteness
 1     C A.DC1           inc      __       0
 2     G A.DG2           22p      !!       0
 3     C A.DC3           23p      !!       0
 4     G A.DG4           32p      1b       0.573
 5     A A.DA5           22p      !!       0
 6     A A.DA6           22p      !!       0
 7     T A.DT7           trig     !!       0
 8     T A.DT8           trig     !!       0
 9     C A.DC9           trig     !!       0
 10    G A.DG10          22p      !!       0
 11    C A.DC11          22p      4b       0.533
 12    G A.DG12          22m      !!       0

 1     C B.DC13          inc      __       0
 2     G B.DG14          trig     !!       0
 3     C B.DC15          trig     !!       0
 4     G B.DG16          32p      1b       0.476
 5     A B.DA17          trig     !!       0
 6     A B.DA18          trig     !!       0
 7     T B.DT19          trig     !!       0
 8     T B.DT20          22p      !!       0
 9     C B.DC21          23p      !!       0
 10    G B.DG22          32p      1b       0.369
 11    C B.DC23          23p      0a       0.015
 12    G B.DG24          33p      1a       0.790


Concatenated suite string per chain. To avoid confusion of lower case
modified nucleotide name (e.g., 'a') with suite cluster (e.g., '1a'),
use --suite-delimiter to add delimiters (matched '()' by default).

1   A DNA nts=12  C!!G!!C1bG!!A!!A!!T!!T!!C!!G4bC!!G
2   B DNA nts=12  C!!G!!C1bG!!A!!A!!T!!T!!C1bG0aC1aG



7
RNA structures (DSSR) / Re: Batch-processing structures with analyze -t
« on: January 06, 2020, 10:26:06 am »
Hi Louis Becquey,

Thanks for using 3DNA/DSSR and for your kind words about it.

You mentioned "analyze -t", which is a program in the classic 3DNA 2.x suite that is current in maintenance mode. You also referred to DSSR, which is a brand-new program I've been actively developing and continuously refining.

For the calculation of eta' and theta' pseudo-torsions, among other things, I'd suggest that you switch to DSSR. Using the --json option, you can easily parse DSSR output. Compared to the "analyze -t" approach, your pipeline would be significantly simplified. See the following two threads:

Hope this helps.

Xiang-Jun


PS: The fixed-name file "Borg_P_C1_C4.dat" is for information only. It is by-product of running the "analyze -t" program. With the source code, you could name the file in a way as you see fit.

8
Quote
Is it Propeller Twist? Roll? Alpha or Beta torsion bond angles?

Interesting questions. Unfortunately, I do not have an answer as to how these parameters (if any) may be related to your research question. You'd need to explore the issue and see what comes out.

Best regards,

Xiang-Jun

9
Sorry, the simple answer is no.

The various parameters associated with each step are context dependent. If you are interested in the trend of certain parameters, you could run 3DNA on your specific dataset, and then extract those parameters for comparison.

Best regards,

Xiang-Jun

10
This website http://skmatic.x3dna.org/ (see screenshot below) aims to showcase DSSR-enabled cartoon-block schematics of nucleic acid structures using PyMOL. It presents a simple interface to browse pre-calculated PDB entries with a set of default settings: long rectangular blocks for Watson-Crick base-pairs, square blocks for G-tetrads in G-quadruplexes, with minor-groove edges in black. Users can also specify an URL to a PDB- or mmCIF-formatted file or upload such an atomic coordinates file directly, and set several common options to customerize to the rendered image.

Moreover, a web API to DSSR-PyMOL schematics is available to allow for its easy integration into third-party tools.


Input a PDB id
Pre-calculated cartoon-block images together with summary information are available for PDB entries of nucleic-acid-containing structures. Note that gigantic structures like ribosomes that are only represented in mmCIF format are excluded from the resource. The base block images are most effective for small to medium-sized structures.

Here are a few examples:
  • 1ehz, the crystal structure of yeast phenylalanine trna at 1.93-A resolution
  • 2lx1, the major conformation of the internal loop 5'GAGU/3'UGAG
  • 2grb, the crystal structure of an RNA quadruplex containing inosine-tetrad
  • 4da3, the crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41
  • 1oct, crystal structure of the Oct-1 POU domain bound to an octamer site
  • 2hoj, the crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions

Each entry is shown with images in six orthogonal perspectives: front, back, right, left, top, bottom. The 'front' image (upper-left in the panel) is oriented into the most-extended view with the DSSR --blocview option. The corresponding PyMOL session file and PDB coordinate file are available for download. One can also visualize the structure interactively via 3Dmol.js.

Sample PDB entries
Users can browse random samples of pre-calculated PDB entries. The number should be between 3 and 99, with a default of 12 entries (see below for an example). Simply click the 'Submit' button or the link "Random samples (3 to 99)" to see random results of 12 entries each time.

Specify an coordinate file
The atomic coordinate file must be in PDB or mmCIF format, and can be optionally gzipped (.gz). One can either specify an URL to or select a coordinate file. Several common options are available to allow for user customizations.

Web API help message
Usage with 'http' (HTTPie):
    http -f http://skmatic.x3dna.org/api [options] url=|model@
    http http://skmatic.x3dna.org/api/pdb/pdb_id  -- for a pre-calculated PDB entry
    http http://skmatic.x3dna.org/api/help        -- display this help message
Options:
    block_file=styles-in-free-text-format [e.g., block_file=wc-minor]
    block_color=nt-selection-and-color    [e.g., block_color='A:pink']
    block_depth=thickness-of-base-block   [e.g., block_depth=1.2]
    r3d_file=true-or-FALSE(default)       [e.g., r3d_file=true]
    raw_xyz=true-or-FALSE(default)        [e.g., raw_xyz=true]
Required parameter
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz]
    model@coordinate-file      [e.g., model@1ehz.cif]
    # Only one must be specified. 'url' precedes 'model' when both are specified.
    # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.
Examples
    http -f http://skmatic.x3dna.org/api block_file='wc-minor' model@1ehz.cif r3d_file=t
    http -f http://skmatic.x3dna.org/api url=https://files.rcsb.org/download/1ehz.pdb.gz -d -o 1ehz.png
    http http://skmatic.x3dna.org/api/pdb/1ehz -d -o 1ehz.png
    # with 'curl'
    curl http://skmatic.x3dna.org/api -F 'model=@1msy.pdb' -F 'block_file=wc-minor' -F 'r3d_file=1'
    curl http://skmatic.x3dna.org/api -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -o 1ehz.png
    curl http://skmatic.x3dna.org/api/pdb/1ehz -o 1ehz.png

Sample images
       

11
Quote
Where do I enter a nucleotide base pair sequence? How do I enter a nucleotide base pair sequence? Like this: ATCGAAGGTC? or like this: A/T/T/C/G/? May I please have a link?

It is not clear (to me at least) what you mean by entering "a nucleotide base pair sequence", without contextual information. In 3DNA, the fiber command allow you to specify a specific base sequence for generic A-, B-, and C-DNA models. Run "fiber -h" for details.

In the Web 3DNA 2.0 website, see the http://web.x3dna.org/index.php/fibermodel section (the top 5 models) for examples.

Best regards,

Xiang-Jun
 


12
Quote
It worked with do_x3dna VMD plugin.

I do not know if it works now. For any do_x3dna specific questions, please ask the authors/developers directly. I was not involved in that project and I cannot provide any practical help for do_x3dna.

Best regards,

Xiang-Jun

13
Quote
I tried with the changes you suggested and it worked.

Glad to hear that the suggested method works. Thanks for the update.

Quote
Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command.

Since you are running 'analyze' in a loop to process multiple PDB files, you should be able to rename the default output file as desired. Without further details, that's all I could say.

Best regards,

Xiang-Jun

14
Hi Tanashreee,

Thanks for using 3DNA and for posting your questions on the Forum.

Quote
I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

Please upgrade to 3DNA v2.4, which detects 12 base-pairs out of the expected 13. Version 2.0 is more than 10 years old, and there is no practical reasons to use it anymore.

3DNA does not detect the ADE-TG pair due to improper labeling of base atoms in the modified TG. See the attached image of the pair, and pay close attention to the TG base ring (e.g., C7 connects to N1 etc.)

Rectify names of the TG base atoms following PDB convention (as for T), 3DNA should then work. Please have a try and report back how it goes.

Best regards,

Xiang-Jun





15
DNA/RNA-protein interactions (SNAP) / Re: About sugar-pi stacking
« on: November 08, 2019, 04:27:51 pm »
Hi Honglue,

Have you found a solution to your sugar-pi stacking task? If so, you are encouraged to share your findings with the 3DNA Forum community. If you have not found a practical solution yet and you are still interested in this topic, I may consider to add this feature to SNAP.

Best regards,

Xiang-Jun

16
DNA/RNA-protein interactions (SNAP) / Re: About sugar-pi stacking
« on: October 17, 2019, 04:55:36 pm »
Hi Honglue,

The current version of SNAP does not detect sugar-pi stacking interaction in DNA-protein complexes. Only 'classic' stacking interactions between base and planar side chains (e.g., ARG, HIS, TRP etc) are reported. This is one of the areas that would be enhanced in futures releases of SNAP.

Regarding DNA-protein interactions in general, you may want to have a look of DNAproDB from the Remo Rohs laboratory. A new paper has just been published in NAR, "DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes".

For sugar-pi stacking in particular, why not ask the authors on how they detected the reported interactions? Hopefully, they may provide directly what you need.

Best regards,

Xiang-Jun

17
MD simulations / Re: Filter frayed ends or broken H bonds
« on: October 11, 2019, 08:54:11 am »
See FAQ entry: "How to fix missing (superfluous) base pairs identified by find_pair?" (http://forum.x3dna.org/faqs/how-to-fix-missing-(superfluous)-base-pairs-identified-by-find_pair/)

Again, if you provide a concrete example, we could discuss the issue in more detail.

Best regards,

Xiang-Jun

18
MD simulations / Re: Filter frayed ends or broken H bonds
« on: October 10, 2019, 09:09:46 am »
Hi Rahul,

Please use concrete examples to illustrate unambiguously what you want to achieve.

Thanks.

Xiang-Jun

19
Hi,

Thanks for providing a detailed example. It is completely fine, even preferable, to use a simplified data set just to illustrate the issue at hand.

With the data files and steps you provided, I can now understand clearly where the issue is. The 3DNA programs are working as expected, but one step is missing. Please try the following:

Code: [Select]
# Create a text file ('rot_yz180', attached), with the following content:
by rotation y 180
by rotation z 180

# transform file 'part-2_aligned.pdb' (attached), as below
rotate_mol -r=rot_yz180 part-2_aligned.pdb part-2_aligned-rotated.pdb

Now use part-2_aligned-rotated.pdb instead of part-2_aligned.pdb in your concatenated file. Have a try and report back how it goes.
 
Xiang-Jun

20
Would it be feasible that you attach all the PDB files? Without those data files, it is impossible to reproduce the reported image and it is hard (for me at least) to pinpoint exactly where the issue is.

Xiang-Jun

21
Please be specific with detailed steps you took and problems you experienced.

Thanks,

Xiang-Jun

22
RNA structures (DSSR) / Re: Wrong junctions
« on: September 30, 2019, 10:39:52 pm »
As a follow-up, I've released DSSR v1.9.7-2019oct01 that's fixed the reported issue.

Xiang-Jun

23
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 11:44:51 pm »
Hi Jun,

I've updated DSSR (still labelled v1.9.6-2019sep16). It should have fixed the junction issue (in the first 3-way junction case) you observed in PDB entry 4wsm. See also my note on junctions with pseudoknots.

Please have a try and report back how it goes. In reporting any further issues, please remain to be specific.

Best regards,

Xiang-Jun

24
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 04:49:28 pm »
Hi Jun

Please provide more details with the additional PDB entries, as you did for 4wsm. I believe the underlying issue is similar, most likely associated with extreme cases with distorted structures. The more detailed cases you provide, the better I can test/validate the fixes for the next DSSR release.

Best regards,

Xiang-Jun

25
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 01:56:52 pm »
Hi Jun,

A junction loop derived by DSSR may share the same stem when pseudoknots are involved, as emphased in the DSSR paper (https://doi.org/10.1093/nar/gkv716). See for example, Figure 4 for the env22 twister ribozyme, PDB id: 4rge. Generally speaking, this is a unique feature, instead of a bug, of DSSR. Such junctions are noted with a suffix * after the serial number. One can get rid of such loops by specifying the --nested option.

I've a quick look of your reported case on 4wsm, and noticed that there may be a bug in DSSR. The first case (a three way junction) should not be there. The issue is due to stem#101 (with 2 base pairs) which has a highly distorted geometry, and judged as parallel by DSSR. I will look into the issue further, and get back to you soon.

In the meantime, you could take it as a special case, or simply remove junctions with a * suffix.

Thanks for reporting the issue!

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.