In early 2015, Thomas Holder (the PyMOL Principal Developer at Schrodinger) and I agreed to work together on connecting DSSR to PyMOL. Moreover, we called for the community’s involvement in writing a DSSR plugin for PyMOL and received a few enthusiastic replies. Over the past few months, many significant progresses have been made in DSSR, including an article titled DSSR: an integrated software tool for dissecting the spatial structure of RNA published in Nucleic Acids Research (NAR) and a more streamlined DSSR-Jmol integration based on the --json output.

From the very beginning, Thomas and I had envisioned that the DSSR-PyMOL integration would include two components: one is to bring DSSR-derived RNA/DNA structural features into PyMOL (similar to the DSSR-Jmol interface, funcationality-wise), and the other is to render DSSR’s simple yet informative base-rectangular representations with PyMOL. While the ‘analysis’ component is a work in progress, the ‘visualization’ part is ready for the community to take advantage of.

Thomas has written a Python script named dssr_block.py. When the script is run in PyMOL, it adds the “dssr_block” command. The dssr_block.py script is less than 100 lines including documentation, with the real code taking no more than half of the total line number. The detailed documentation section (with two examples), when condensed, is as follows:

DESCRIPTION
    Create a nucleid acid cartoon with DSSR
USAGE
    dssr_block [selection [, state [, block_file [, block_depth [, name [, exe]]]]]]
ARGUMENTS
    selection = str: atom selection {default: all}
    state = int: object state (0 for all states) {default: -1, current state}
    block_file = face|edge|wc|equal|minor|gray {default: face}
    block_depth = float: thickness of rectangular blocks {default: 0.5}
    name = str: name of new CGO object {default: dssr_block##}
    exe = str: path to "x3dna-dssr" executable {default: x3dna-dssr}
EXAMPLE
    fetch 1ehz, async=0
    as cartoon
    dssr_block
    set cartoon_ladder_radius, 0.1
    set cartoon_ladder_color, gray
    set cartoon_nucleic_acid_mode, 1
    # multi-state
    fetch 2n2d, async=0
    dssr_block 2n2d, 0
    set all_states

Download the dssr_block.py script into a folder (directory) of your choice. Within PyMOL command window, type:

run dssr_block.py  # to make the 'dssr_block' command avaible
help dssr_block    # to get the help message, with contents shown above

The resultant cartoon-block image for running the documented commands (except for the additional orient command for best view) for case 1ehz is shown in Fig. 1 below.

Fig. 1: Cartoon-block image generated by dssr_block.py for PDB entry 1ehz (yeast phenylalanine tRNA)

For the NMR ensemble 2n2d, the corresponding image (after running orient) is illustrated in Fig. 2 as follows:

Fig. 2: Cartoon-block image generated by dssr_block.py for PDB entry 2n2d (an NMR ensemble).

In addition to the default settings, DSSR offers quite a few variations for the size and coloring of rectangular blocks, as demonstrated in Fig.3. The main settings are through the block_file option in PyMOL (note the underscore), corresponding to DSSR --block-file (or --block_file). The corresponding PyMOL commands are also listed for your reference. You can easily play around with the various styles interactively in PyMOL by toggling objects (dssr_block##) on or off. Enjoy!

Fig. 3: Cartoon-block image generated by dssr_block.py for PDB entry 355d (the Dickerson B-DNA dodecamer).

Fig. 3 is created with the following PyMOL commands:

reinitialize
fetch 355d, async=0
bg_color white

as cartoon
orient
turn z, -90
turn y, 180

set cartoon_ladder_mode, 1
set cartoon_ladder_radius, 0.1
set cartoon_ladder_color, black

set cartoon_tube_radius, 0.5
set cartoon_nucleic_acid_mode, 1
set cartoon_color, gold

dssr_block 355d                  # default base blocks in solid color
dssr_block block_file=edge       # rectangular blocks in wireframe (black)
dssr_block block_file=face+edge  # solid color with outline
dssr_block block_file=equal      # bases blocks in equal size
dssr_block block_file=minor      # with minor-groove colord black
dssr_block block_file=wc         # Watson-Crick base pairs in long bp blocks
dssr_block block_file=wc-minor   # Watson-Crick pairs + minor-groove edge
dssr_block block_file=gray       # rectangular blocks all in gray
dssr_block block_depth=1.8       # with increased thickness

Notes

• The dssr_block.py script described here is the original version Thomas communicated to me. Current version of this script and related topics can be found in the Dssr block PyMOLWiki page.
• For this script to work, DSSR needs to be installed and x3dna-dssr in the PATH.
• In PyMOL, set cartoon_nucleic_acid_mode, 1 employs C3′ instead of the default P (‘mode 0’) for the smooth backbone trace. Since 5′ terminal phosphate groups are normally not available from X-ray crystal structures (e.g., 355d), ‘mode 1’ is used to avoid orphan base blocks from the backbone trace.

As of today (2016-01-16), the number of registrations on the 3DNA Forum has reached 2,562. Moreover, all the members (as far as I can tell) are legitimate since the Forum has remained spam free. From the very beginning, ensuring a high information-to-noice ratio has been a top priority. The goal has been achieved by taking the following measures:

State the rules clearly in the “Registration Agreement”

This forum is dedicated to topics generally related to the 3DNA suite of software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. To make the 3DNA forum a more pleasant virtual community for all of us to learn from and contribute to, please be considerate and practice good netiquette (http://www.albion.com/netiquette/).

I strive to make the forum spam free. Specifically, posts that are not 3DNA related in the broad sense are taken as spams, and are strictly forbidden. You are solely responsible for the content of your posts. We reserve the right to remove any post deemed as inappropriate, deactivate the account and ban the IP address of any abuser of the forum, WITHOUT NOTICE.

When posting on the Forum, please abide by the following rules: …

In a nutshell, you are welcome to participate and should not hesitate to ask questions, but remember to play nice and preferably share what you’ve learned! Please note that we do not tolerate spamming or off-topic trolling of any form.

Take advantage of anti-spam software

In additional to the verification of email address and check for black-listed IP addresses, the topic-specific questions have been very effective. Three examples of such questions are shown below:

What does the 'A' in 3DNA stand for? (hint: 4-char long)

How many standard bases does RNA have (hint: 1-digit number)

What is the value of the expression (3.1498 * 0 + 168)?

Overall, I do not like CAPTCHA — I’ve found the highly-distorted images in some websites especially troublesome. For the first few of years (to ~2014), the 3DNA Forum did not contain a captcha image in the registration page. Later on, however, I’ve noticed quite a few spam registrations/posts. In addition to quickly cleaning them up manually, I had refined the topic-specific questions, and turned on the visual verification image at level “Medium — Overlapping colored letters, with noise/lines”. Experience over the past couple of year has demonstrated the effectiveness of the combined strategy. As shown in the screen capture below, as of this writing, 177,562 spammers have been blocked by the anti-spam software!

Verify and approve ‘suspect’ accounts quickly

The above mentioned anti-spaming measures have blocked virtually all the “bad guys” so I do not need to waste time fighting them. I receive an email notification for each successful registration. The vast majority of registrants can then immediately access the member-only download section or post questions on the 3DNA Forum after registration. A significant portion (~1 out of 6) of the registrations, however, would be masked as suspicious and need my action. The email message for such cases reads like this:

‘xxxx’ has just signed up as a new member of your forum. Click the link below to view their profile. …
Before this member can begin posting they must first have their account approved. Click the link below to go to the approval screen. …

Wherever I have access to the Internet (including after hours with an iPad Air 2), I’ve always been quick in verifying and (mostly) approving these registrations.

Overall, since http://forum.x3dna.org was created in December 2011, the Forum has received significant attention in the field of DNA/RNA structural bioinformatics. As the community begins to appreciate and fully take advantage of what DSSR and SNAP have to offer, I have no doubt the Forum will gain even wider-spread recognition.

In recent years, reproducibility of ‘scientific’ publications has become quite a topic. See a recent essay Five selfish reasons to work reproducibly by Markowetz in Genome Biology (2015, 16:274). There are numerous reasons why reproducibility could become an issue at all in science. What I have continuously strived for in my scientific career, however, is to ensure that my published results are reproducible. As a concrete example, I created a dedicated section titled DSSR-NAR paper on the 3DNA Forum that provides full details (scripts and data files) so that any interested parties can rigorously reproduce the results reported in the DSSR Nucleic Acids Research (NAR) paper.

In my support of 3DNA for over a decade, the #1 issue I experienced is undoubtedly vague (non-reproducible) questions. For example, I have recently been asked via email why the 3DNA find_pair/analyze programs miss “some basepair … even though it is in the pdb file”. Without access to the PDB file to reproduce the problem, however, I cannot provide a concrete answer. In an effect to prevent ambiguous questions, I made the following explicit point in the “Registration Agreement” of the 3DNA Forum (no. 2 on the list):

Be specific with your questions; provide a minimal, reproducible example if possible; use attachments where appropriate.

The #2 issue is receiving 3DNA-related questions privately instead of on the intended public 3DNA Forum. I turned off “personal messaging” to receive private messages on the Forum long time ago, yet I have kept receiving questions via emails. In several locations on the 3DNA Forum, I have made this ‘public-question’ policy crystal clear:

Ask your questions in the public 3DNA forum instead of sending xiangjun emails or personal messages. (no. 1 on the ‘Registration Agreement’)

Please be aware that for the benefit of the 3DNA-user community at large, I do not provide private email/personal message support; the forum has been created specifically for open discussions of all 3DNA-related issues. In other words, any 3DNA-associated questions are welcome and should be directed here. Presumably I’ve made the message simple and clear enough to get across without further explanation. (in ‘Site announcements » Download instructions’ and ‘Downloads » 3DNA download’)

In response to the many 3DNA-related questions that still keep coming via email, I created the following entry of Canned Responses in gmail:

Thanks for your interest in using 3DNA. Please be aware that for the benefit of the 3DNA-user community at large, I do not provide private email support; the 3DNA Forum (http://forum.x3dna.org/) has been created specifically for open discussions of all 3DNA-related issues. In other words, any 3DNA-associated questions are welcome and should be directed there. I monitor the forum regularly and respond to posts promptly.

I look forward to seeing you on the 3DNA Forum (http://forum.x3dna.org/).

Overall, I’ve learned from experience that addressing reproducible questions publicly does the best for the 3DNA community. Users can register with personal (free) email address, and post simulated data to illustrate the problem at hand. Moreover, questions on the Forum have always received quick responses. Over time, the Forum has served as an archive that everyone can benefit from.

With the foundation laid by the previous two posts on Fitting of base reference frame and Automatic identification of nucleotides, we can now get into the details on how the ‘simple’ base-pair (bp) parameters are derived. To make the point clear, I am using two concrete examples from the yeast phenylalanine tRNA (PDB id: 1ehz): the first pair is 2MG10+G45, of type M+N (shortened to g+G) in 3DNA/DSSR; and the second example is a Watson-Crick pair U6–A67, of type M–N (shortened to U–A).

Pair 2MG10+G45 (g+G, of type M+N, see Fig. 1)

Base reference frames

Fig. 1: Base pair 2MG10+G45 (g+G) of type M+N in yeast phenylalanine tRNA 1ehz

In the original coordinate system (as in 1ehz.pdb downloaded from the RCSB PDB), the base-reference frames for 2MG10 and G45 are:

# base reference frame of 2MG10
{
  "rsmd": 0.018218,
  "origin": [65.696016, 45.134944, 18.125044],  # o1
  "x_axis": [0.690346, 0.713907, -0.117302],    # x1
  "y_axis": [-0.706849, 0.700116, 0.101003],    # y1
  "z_axis": [0.154232, 0.013188, 0.987947]      # z1
}
# base reference frame of G45
{
  "rsmd": 0.025865,
  "origin": [70.584399, 50.526567, 17.229626],  # o2
  "x_axis": [0.818521, 0.49914, -0.284399],     # x2
  "y_axis": [-0.574112, 0.728382, -0.373973],   # y2
  "z_axis": [0.020486, 0.469381, 0.882758]      # z2
}

The base-pair reference frame

Since dot(z1, z2) = 0.88 (positive), this pair is of type M+N in 3DNA/DSSR. The ‘mean’ z-axis of the pair is the average of z1 and z2, which is z = [0.090069, 0.248769, 0.964366] (normalized). This is the z-axis of the bp frame, as in 3DNA/DSSR.

The ‘long’ axis employs RC8 (purines) and YC6 (pyrimidines) base atoms. Here 2MG10 and G45 are all purines, so the following two C8 atoms are used:

# C8 atoms of 2MG10 and G45 in 1ehz
HETATM  208  C8  2MG A  10      62.199  48.621  18.635  1.00 40.38           C
ATOM    987  C8    G A  45      67.772  54.149  15.386  1.00 40.45           C

The vector from C8 of G45 to C8 of 2MG10 is:

y0 = [62.199  48.621  18.635] - [67.772  54.149  15.386]
   = [-5.573  -5.528   3.249]

Normally, y0 and z-axis are not orthogonal. Here they have an angle of ~81º. The orthogonal component of y0 with reference to the z-axis, when normalized, is the y-axis:

y = [-0.676751, -0.695120, 0.242520]

The x-axis is defined by the right-handed rule:

x = [-0.730682, 0.674479, -0.105746]

Overall, the orthonormal x-, y- and z-axes of the pair defined thus far are:

x = [-0.730682, 0.674479, -0.105746]
y = [-0.676751, -0.695120, 0.242520]
z = [0.090069, 0.248769, 0.964366]

Derivation of the six ‘simple’ base-pair parameters (Fig. 2)

Fig. 2: Schematic diagram of six rigid-body base-pair parameters

Propeller is the ‘torsion’ angle of z2 to z1 with reference to the y-axis, and is calculated using the method detailed in the blog post How to calculate torsion angle?. Here Propeller is: -24.24º. Similarly, Buckle is defined as the ‘torsion’ angle of z2 to z1 with reference to the x-axis, and is -14.81º. Opening is defined as the angle from y2 to y1 with reference to the z-axis, and is: 13.32º.

The corresponding translational parameters are simply projects of the o2 to o1 vector onto the x-, y- and z-axis, respectively. Here, they have values:

d = o1 - o2 = [-4.888383, -5.391623, 0.895418]
Shear = dot(d, x) = -0.16
Stretch = dot(d, y) = 7.27
Stagger = dot(d, z) = -0.92

‘Corrections’ of Buckle and Propeller

Base-pair non-planarity is due to the following three parameters: Buckle, Propeller, and Stagger. In particular, Buckle and Propeller cause the two bases to be non-parallel, the most noticeable characteristic of a pair. These two angular parameters are well-documented in literature, even among the canonical Watson-Crick base pairs. In 3DNA/DSSR, the angle between the two base normal vectors (in range [0, 90º]) is related to Buckle and Propeller with the formula:

interBase-angle = sqrt(Buckle^2+Propeller^2)

For the 2MG10+G45 pair, the angle between z1 and z2 is 28.18º, and sqrt(Buckle^2+Propeller^2) = 28.405º. So the following ‘corrections’ are made:

Buckle = -14.81 * 28.18 / 28.405 = -14.69
Propeller = -24.24 * 28.18 / 28.405 = -24.05

Overall, the ‘corrections’ have only small influence on the numerical values of the reported Buckle and Propeller parameters. It is ‘sensible’ that the ‘simple’ parameters have the property interBase-angle = sqrt(Buckle^2+Propeller^2), just as the original 3DNA/DSSR bp parameters.

Now, the six ‘simple’ bp parameters for 2MG10+G45, reported in 3DNA analyze program as of v2.3-2016jan01 are:

Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
*    1 g+G      -0.16      7.27     -0.92    -14.69    -24.05     13.32   28.2

The corresponding local bp parameters as originally reported by 3DNA/DSSR are as follows. Note the significant differences in Shear vs. Stretch, and Buckle vs. Propeller in the two sets of bp parameters. On the other hand, Stagger is identical and Opening should be quite close, by definition. Due to the similarity in Stagger and Opening, DSSR only reports four ‘simple’ parameters (i.e., Shear, Stretch, Buckle, and Propeller).

Local base-pair parameters
     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
    1 g+G      -7.21     -0.97     -0.92     25.58    -11.83     13.07

Base-pair U6–A67 (Watson-Crick U–A, of type M–N, see Fig. 3)

Fig. 3: Base pair U6–A67 (U–A) of type M–N in yeast phenylalanine tRNA 1ehz

Base reference frames

In the original coordinate system (as in 1ehz.pdb downloaded from the RCSB PDB), the base-reference frames for U6 and A67 are:

# base reference frame of U6 (white in Fig. 3)
{
  "rsmd": 0.010835,
  "origin": [60.441988, 48.83479, 41.242523],  # o1
  "x_axis": [0.28491, 0.503019, 0.815965],     # x1
  "y_axis": [0.887155, -0.460753, -0.025726],  # y1
  "z_axis": [0.363018, 0.731217, -0.577529]    # z1
}
# base reference frame of A67 (colored yellow in Fig. 3)
{
  "rsmd": 0.01992,
  "origin": [60.578326, 48.823104, 41.154211], # o2
  "x_axis": [0.034097, 0.205538, 0.978055],    # x2
  "y_axis": [-0.90687, 0.417653, -0.056155],   # y2
  "z_axis": [-0.420029, -0.885054, 0.200637]   # z2
}

The base-pair reference frame

Since dot(z1, z2) = -0.92 (negative), this pair is of type M–N in 3DNA/DSSR. The y- and z-axis are thus reversed (corresponding to a 180º rotation around the x-axis) to align z2 with z1.

# base reference frame of A67, with y- and z-axes reversed
{
  "origin": [60.578326, 48.823104, 41.154211], # o2
  "x_axis": [0.034097, 0.205538, 0.978055],    # x2
  "y_axis": [0.90687, -0.417653, 0.056155],    # y2 -- reversed
  "z_axis": [0.420029, 0.885054, -0.200637]    # z2 -- reversed
}

Thereafter, the procedure is similar to the one for the M+N type above. Note here U6 is a pyrimidine, so its C6 atom is used. The final results are:

# C6 atom of U6 and C8 atom A67 in 1ehz
ATOM    132  C6    U A   6      64.926  46.497  41.084  1.00 35.72           C  
ATOM   1457  C8    A A  67      56.129  50.866  40.893  1.00 40.04           C  
#--------- 
y0 = [64.926  46.497  41.084] - [56.129  50.866  40.893]
   = [8.797  -4.369   0.191]
x = [0.160777, 0.363836, 0.917482]
y = [0.902274, -0.430972, 0.012793]
z = [0.400064, 0.825764, -0.397570]

The six ‘simple’ and original base-pair parameters

Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
     1 U-A       0.06     -0.13     -0.08     -0.59    -23.71      5.39   23.7
# ------------
Local base-pair parameters
     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
    1 U-A       0.06     -0.13     -0.08     -0.63    -23.71      5.50

As can be seen, for Watson-Crick pairs, the ‘simple’ and the original bp parameters are very similar.

Special notes on the ‘simple’ base-pair parameters

• For the most common Watson-Crick pairs, the newly introduced ‘simple’ bp parameters match those of the original 3DNA/DSSR parameters very well (as shown by the U6–A67 pair). For non-canonical pairs, significant differences in Shear, Stretch, Buckle and Propeller are expected (as illustrated by the 2MG10+G45 pair). The differences come from the divergent definitions of the bp reference frame, which is distinct for each type of non-canonical pairs.
• Only the original 3DNA/DSSR six bp parameters can be used for exact reconstruction (with the 3DNA rebuild program) of the corresponding bp geometry. The ‘simple’ bp parameters are for description only, and they could be more intuitive than the original 3DNA/DSSR counterparts. They complement, buy by no means replace, the classic “local” bp parameters. The term ‘simple’ is used to distinguish the new from the original closely related, yet quite different bp parameters.
• As details for the 2MG10+G45 pair, several ad hoc decisions are made in deriving the ‘simple’ bp parameters. For example, instead of using RC8–YC6 to define the y-axis, one can also use RN9–YN1 (as did by Richardson). Each such choice will lead (slightly) different numerical values, depending on the type of the non-canonical pairs. In some cases, Buckle and Propeller could differ by several degrees. Since RC8 and YC6 atoms lie near the ‘center’ of purines and pyrimidines, they are used to define the y-axis (by default). DSSR has provisions of selecting RN9–YN1, as well as a couple of other choices, for the definition of the y-axis.
• When the M+N pair is counted as N+M, Shear, Stretch, Buckle, and Propeller remain the same, but Stagger and Opening reverse their signs. For example, here are the results of 2MG10+G45 vs. G45+2MG10:

# 2MG10+G45
Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
*    1 G+g      -0.16      7.27      0.92    -14.69    -24.05    -13.32   28.2
# Reverse the order: treated as G45+2MG10
Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
*    1 g+G      -0.16      7.27     -0.92    -14.69    -24.05     13.32   28.2

• When the M–N pair is counted as N–M, Stretch, Stagger, Propeller, and Opening remain the same, but Shear and Buckle reverse their signs. For example, here are the results of U6–A67 vs. A67–U6:

# U6–A67
Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
     1 U-A       0.06     -0.13     -0.08     -0.59    -23.71      5.39   23.7
# Reverse the order: treated as A67–U6
Simple base-pair parameters based on YC6-RC8 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening  angle
     1 A-U      -0.06     -0.13     -0.08      0.59    -23.71      5.39   23.7

Related posts

• Fitting of base reference frame
• Automatic identification of nucleotides
• ‘Simple’ parameters for non-Watson-Crick base pairs
• Simple base-pair parameters
• Quantifying base-pair geometry by six rigid-body parameters
• How to calculate torsion angle?

Once a nucleotide (nt) is identified, and matched to A (C, G, T, U) for the standard case or a (c, g, t, u) for a modified one, 3DNA/DSSR performs a least-squares fitting procedure to locate the base reference frame in three-dimensional space. The basic idea is very simple and widely applicable. The algorithm constitutes one of the key components of 3DNA/DSSR. As always, the details can be most effectively illustrated with a worked example. Using G1 in the yeast phenylalanine tRNA (PDB id: 1ehz) as an example, the atomic coordinates of its nine base-ring atoms are:

# G1, nine base-ring atoms for ls-fitting
ATOM     14  N9    G A   1      51.628  45.992  53.798  1.00 93.67           N  
ATOM     15  C8    G A   1      51.064  46.007  52.547  1.00 92.60           C  
ATOM     16  N7    G A   1      51.379  44.966  51.831  1.00 91.19           N  
ATOM     17  C5    G A   1      52.197  44.218  52.658  1.00 91.47           C  
ATOM     18  C6    G A   1      52.848  42.992  52.425  1.00 90.68           C  
ATOM     20  N1    G A   1      53.588  42.588  53.534  1.00 90.71           N  
ATOM     21  C2    G A   1      53.685  43.282  54.716  1.00 91.21           C  
ATOM     23  N3    G A   1      53.077  44.429  54.946  1.00 91.92           N  
ATOM     24  C4    G A   1      52.356  44.836  53.879  1.00 92.62           C  

The corresponding nine base-ring atoms of G in its standard base reference frame are listed below. See Table 1 of the report A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry, and file Atomic_G.pdb distributed with 3DNA ($X3DNA/config/Atomic_G.pdb). In DSSR, the content has been integrated into the source code to make the program self-contained.

# G in standard base reference frame
ATOM      2  N9    G A   1      -1.289   4.551   0.000
ATOM      3  C8    G A   1       0.023   4.962   0.000
ATOM      4  N7    G A   1       0.870   3.969   0.000
ATOM      5  C5    G A   1       0.071   2.833   0.000
ATOM      6  C6    G A   1       0.424   1.460   0.000
ATOM      8  N1    G A   1      -0.700   0.641   0.000
ATOM      9  C2    G A   1      -1.999   1.087   0.000
ATOM     11  N3    G A   1      -2.342   2.364   0.001
ATOM     12  C4    G A   1      -1.265   3.177   0.000

A least-squares fitting of the standard onto the experimental set of base-ring atoms defines the base reference frame (Fig. 1). The information is available via the following commands:

# find_pair -s 1ehz.pdb # in file 'ref_frames.dat'
...     1 G   # A:...1_:[..G]G
   53.7571    41.8678    52.9303  # origin
   -0.2589    -0.2496    -0.9331  # x-axis
   -0.5430     0.8365    -0.0731  # y-axis
    0.7988     0.4878    -0.3521  # z-axis
# --------
# x3dna-dssr -i=1ehz.pdb --json | jq .nts[0].frame
{
  rsmd: 0.008,
  origin: [53.757, 41.868, 52.93],
  x_axis: [-0.259, -0.25, -0.933],
  y_axis: [-0.543, 0.837, -0.073],
  z_axis: [0.799, 0.488, -0.352]
}

Fig. 1: G1 in tRNA 1ehz, with base reference frame attached

Please note the following subtle points:

• The standard base (Atomic_G.pdb) is already set in its reference frame: the z-coordinates are virtually zeros, y-coordinates are positive, the atoms along the minor-groove edge have negative x-coordinates, as can be visualized clearly from the attached coordinate frame. In 3DNA, the five standard standard bases are in stored in files Atomic_[ACGTU].pdb, and the corresponding modified ones are in Atomic_[acgtu].pdb. For simplicity, Atomic_A.pdb and Atomic_a.pdb are the same by default, as are the other four cases.

• The translation and rotation of the least-squares fitting process define the experimental base reference frame (for G1 in the above example), and its three axes are orthonormal by definition.

• By design, the base rings of Atomic_A.pdb and Atomic_G.pdb match each other closely (see below), as are the pyrimidines bases. The least-square fitted root-mean-square deviation (rmsd) of the nine base-ring atoms between standard A and G is only 0.04 Å. Fitting the standard A (instead of G) onto G1 of 1ehz leads to a base reference frame that is essentially indistinguishable from the one above (see below). This feature shows that any ambiguity in assigning modified purines to A or G, or pyrimidines to C, T, or U causes no notable differences in 3DNA/DSSR results.

Comparison of base-ring atomic coordinates in standard G and A
          Atomic_G.pdb                         Atomic_A.pdb
N9 G   -1.289   4.551   0.000   |   N9  A   -1.291   4.498   0.000
C8 G    0.023   4.962   0.000   |   C8  A    0.024   4.897   0.000
N7 G    0.870   3.969   0.000   |   N7  A    0.877   3.902   0.000
C5 G    0.071   2.833   0.000   |   C5  A    0.071   2.771   0.000
C6 G    0.424   1.460   0.000   |   C6  A    0.369   1.398   0.000
N1 G   -0.700   0.641   0.000   |   N1  A   -0.668   0.532   0.000
C2 G   -1.999   1.087   0.000   |   C2  A   -1.912   1.023   0.000
N3 G   -2.342   2.364   0.001   |   N3  A   -2.320   2.290   0.000
C4 G   -1.265   3.177   0.000   |   C4  A   -1.267   3.124   0.000

Comparison of G1 (1ehz) base reference frame derived using standard G or A
             Atomic_G.pdb                |             Atomic_A.pdb
 53.7571    41.8678    52.9303  # origin | 53.7286    41.9276    52.9482  # origin
 -0.2589    -0.2496    -0.9331  # x-axis | -0.2562    -0.2540    -0.9327  # x-axis
 -0.5430     0.8365    -0.0731  # y-axis | -0.5444     0.8352    -0.0780  # y-axis
  0.7988     0.4878    -0.3521  # z-axis |  0.7988     0.4878    -0.3522  # z-axis

Related topics:

• Least-squares fitting procedures with illustrated examples
• Automatic identification of nucleotides
• A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry

Any analysis of nucleic acid structures start with the identification of nucleotides (nts), the basic building unit. As per the PDB convention, each nt (like any other ligands) is specified by a three-letter identifier. For example, the four standard RNA nts are ..A, ..C, ..G, and ..U, respectively. The four corresponding standard DNA nts are .DA, .DC, .DG, and .DT, respectively. Note that here, for visualization purpose, each space is represented by a dot (.). In practice, the following codes for the five standard DNA/RNA nts — ADE, CYT, GUA, THY, and URA — are also commonly encountered, among other variants.

On top of the standard nts, there are numerous modified ones, each assigned a unique three-letter code. In the classic yeast phenylalanine tRNA (PDB id: 1ehz), 14 out of the 76 nts are modified, as shown in Fig. 1 below.

Fig. 1: Modified nucleotides in yeast phenylalanine tRNA 1ehz

It is challenging to maintain a comprehensive and updated list of ever-inceasing nts encountered in the PDB and molecular dynamics (MD) simulation packages (e.g., AMBER, GROMACS, and CHARMM). Thus, as of today, some well-known DNA/RNA structural bioinformatics tools can handle only standard nts or a limited list of modified ones.

From early on in the development of 3DNA, I observed that all recognized nts have a core six-membered ring, with atoms named N1,C2,N3,C4,C5,C6 consecutively (see Fig. 2 below). Purines have three additional atoms, named N7,C8,N9. So it is feasible to automatically identify nts, and classify them as pyrimidines and purines, based on the common core skeleton shared by all of them. Moreover, the ‘skeleton’ is not effected by any possible tautomeric or protonation state.

Fig. 2: Identification of nts in 3DNA/DSSR based on atomic names and planar geometry

Early versions of 3DNA employed only three atoms (N1, C2 and C6) and three distances to decide a nt. Purines were further discriminated by the N9 atom, and the N1–N9 distance. While developing DSSR, I revised the nt-identification algorithm by using a least-squares fitting procedure that makes use of all available base ring atoms instead of selected ones. The same new algorithm has also been adapted into the find_pair/analyze etc programs in 3DNA, as of v2.2.

As always, the idea can be best illustrated with a worked example. Guanine in its standard base reference frame, with the following list of nine ring atoms coordinates, is chosen for the least-squares fitting. See file Atomic_G.pdb in the 3DNA distribution, and also Table 1 of the report A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry.

ATOM      2  N9    G A   1      -1.289   4.551   0.000
ATOM      3  C8    G A   1       0.023   4.962   0.000
ATOM      4  N7    G A   1       0.870   3.969   0.000
ATOM      5  C5    G A   1       0.071   2.833   0.000
ATOM      6  C6    G A   1       0.424   1.460   0.000
ATOM      8  N1    G A   1      -0.700   0.641   0.000
ATOM      9  C2    G A   1      -1.999   1.087   0.000
ATOM     11  N3    G A   1      -2.342   2.364   0.001
ATOM     12  C4    G A   1      -1.265   3.177   0.000

By using a ls-fitting procedure, only (any) three atoms are needed. We no longer need to make explicit selection, as we did previously (N1,C2,C6 and N9), thus allowing for possible modification on these atoms.

Using four nts (G1, 2MG10, H2U16, and PSU39, see Fig. 1 above top) of 1ehz as examples, the following list gives the atomic coordinates of base ring atoms, and root-mean-squres devisions (rmsd) of the least-squares fit. Of course, when performing least-squares fitting, the names of corresponding atoms must match (note the different ordering of atoms for H2U and PSU in the list vs the above standard G reference).

#G1, rmsd=0.008
ATOM     14  N9    G A   1      51.628  45.992  53.798  1.00 93.67           N  
ATOM     15  C8    G A   1      51.064  46.007  52.547  1.00 92.60           C  
ATOM     16  N7    G A   1      51.379  44.966  51.831  1.00 91.19           N  
ATOM     17  C5    G A   1      52.197  44.218  52.658  1.00 91.47           C  
ATOM     18  C6    G A   1      52.848  42.992  52.425  1.00 90.68           C  
ATOM     20  N1    G A   1      53.588  42.588  53.534  1.00 90.71           N  
ATOM     21  C2    G A   1      53.685  43.282  54.716  1.00 91.21           C  
ATOM     23  N3    G A   1      53.077  44.429  54.946  1.00 91.92           N  
ATOM     24  C4    G A   1      52.356  44.836  53.879  1.00 92.62           C  

#2MG10, rmsd=0.018
HETATM  207  N9  2MG A  10      61.581  47.402  18.752  1.00 42.14           N  
HETATM  208  C8  2MG A  10      62.199  48.621  18.635  1.00 40.38           C  
HETATM  209  N7  2MG A  10      63.494  48.534  18.422  1.00 40.70           N  
HETATM  210  C5  2MG A  10      63.745  47.167  18.395  1.00 43.82           C  
HETATM  211  C6  2MG A  10      64.965  46.449  18.205  1.00 43.45           C  
HETATM  213  N1  2MG A  10      64.767  45.086  18.293  1.00 44.71           N  
HETATM  214  C2  2MG A  10      63.541  44.482  18.486  1.00 47.21           C  
HETATM  217  N3  2MG A  10      62.411  45.125  18.614  1.00 45.85           N  
HETATM  218  C4  2MG A  10      62.574  46.451  18.582  1.00 43.27           C  

#H2U16, rmsd=0.188
HETATM  336  N1  H2U A  16      77.347  53.323  34.582  1.00 91.19           N  
HETATM  337  C2  H2U A  16      76.119  52.865  34.160  1.00 92.39           C  
HETATM  339  N3  H2U A  16      75.123  52.894  35.107  1.00 93.28           N  
HETATM  340  C4  H2U A  16      75.289  52.711  36.458  1.00 93.34           C  
HETATM  342  C5  H2U A  16      76.696  52.479  36.909  1.00 93.77           C  
HETATM  343  C6  H2U A  16      77.717  53.238  36.039  1.00 93.22           C  

#PSU39, rmsd=0.004
HETATM  845  N1  PSU A  39      74.080  36.066   5.459  1.00 75.82           N  
HETATM  846  C2  PSU A  39      74.415  36.835   4.354  1.00 75.59           C  
HETATM  847  N3  PSU A  39      75.735  36.769   3.984  1.00 76.29           N  
HETATM  848  C4  PSU A  39      76.728  36.038   4.591  1.00 77.28           C  
HETATM  849  C5  PSU A  39      76.307  35.280   5.732  1.00 77.93           C  
HETATM  850  C6  PSU A  39      75.025  35.316   6.112  1.00 76.07           C  

As noted in the DSSR paper, the rmsd is normally <0.1 Å since base rings are rigid. To account for experimental error and special non-planar cases, such as H2U in 1ehz, the default rmsd cutoff is set to 0.28 Å by default.

With the above detailed algorithm, DSSR (and the 3DNA find_pair/analyze programs) can automatically identify virtually all ‘recognizable’ nts in the PDB. A survey performed in June 2015 detected 630 different types of modified nucleotides in the PDB.

It is worth noting the following points:

• The choice of standard G instead of A as the reference base has no impact on the results. As a matter of fact, the rmsd between G and A is only 0.04 Å. Note also the generous default cutoff of 0.28 Å.
• The method obviously depends on proper naming of the ring atoms. Specially, the base ring atoms must be named N1,C2,N3,C4,C5,C6 consecutively, with purines having three additional atoms named N7,C8,N9. Thus, under this scheme, TPP (thiamine diphosphate) would not be recognized as a nt by default, simply because of the extra prime (′) of atoms in the six-membered ring. In nucleic acid structures, the prime symbol is normally associated with atoms of the sugar moiety (e.g., the C5′ atom).

Fig. 3: TPP (thiamine diphosphate) would not be recognized as a nt.

• On the other hand, nt cofactors in an otherwise ‘pure’ protein structure will also be recognized. One example is the two AMP (adenosine monophosphate) ligands in PDB entry 12as. This extra identification of nts does no harm in such cases. As shown in the analysis of the SAM-I riboswitch in the DSSR paper, taking the SAM ligand as a nt in base triplet recognition is a neat feature.

• Once a nucleotide has been identified and classified into purines and pyrimidines, exocyclic atoms can be used for further assignment: O6 or N2 distinguishes guanine from adenine, N4 separates cytosine from thymine and uracil, and C7 (or C5M, the methyl group) differentiates thymine from uracil. For some modified nts, the distinctions within purines or pyrimidines may not be that obvious. For example, inosine may be taken as a modified guanine or adenine. However, this ambiguity does not pose any significant effect on the calculated base-pair parameters.

• In DSSR and 3DNA, each identified nt is assigned a one-letter shorthand code: the standard ..A, .DA, and ADE (among a few other common variations) is shortened to upper-case A, and similarly for C, G, T, and U. Modified nts, on the other hand, are shortened to their corresponding lower-case symbol. For example, modified guanine such as 2MG and M2G in the yeast phenylalanine tRNA (see Fig. 1 above) is assigned g. So in 3DNA/DSSR output, the upper and lower cases of bases (e.g., nts=3 gCG A.2MG10,A.C25,A.G45) convey special meanings.

Related topics:

• Least-squares fitting procedures with illustrated examples
• Fitting of base reference frame
• A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry

As of v2.3-2016jan01, the 3DNA analyze program outputs a list of new ‘simple’ base-pair and step parameters, by default. Shown below is a sample output for PDB entry 1xvk. This echinomycin-(GCGTACGC)2 complex has a single DNA strand as the asymmetric unit. 3DNA needs the the biological unit (1xvk.pdb1) to analyze the duplex (with the -symm option). This structure contains two Hoogsteen base pairs, and has popped up on the 3DNA Forum for the zero or negative Rise values. Note that the ‘simple’ Rise values are all positive; for the middle (#4) TA/TA step, it is now 3.09 Å instead of 0.

# find_pair -symm 1xvk.pdb1 1xvk.bps
# analyze -symm 1xvk.bps
#   OR by combing the above two commands:
# find_pair -symm 1xvk.pdb1 | analyze -symm
# The output is in file '1xvk.out'
This structure contains 4 non-Watson-Crick (with leading *) base pair(s)
----------------------------------------------------------------------------
Simple base-pair parameters based on RC8--YC6 vectors
      bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
*    1 G+C      -3.07      1.55     -0.35     -6.98      0.29     67.33
     2 C-G       0.27     -0.17      0.35    -22.34      3.33     -2.80
     3 G-C      -0.39     -0.17      0.41     22.91      1.81     -2.73
*    4 T+A      -3.29      1.56      0.31     -8.03      1.59    -70.46
*    5 A+T      -3.29      1.56     -0.31     -8.03      1.59     70.46
     6 C-G       0.39     -0.17      0.41    -22.91      1.81     -2.72
     7 G-C      -0.27     -0.17      0.35     22.34      3.32     -2.80
*    8 C+G      -3.07      1.55      0.35     -6.98      0.30    -67.33
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       ave.     -1.59      0.69      0.19     -3.75      1.75     -1.38
       s.d.      1.72      0.92      0.32     17.57      1.15     52.11
----------------------------------------------------------------------------
Simple base-pair step parameters based on consecutive C1'-C1' vectors
      step       Shift     Slide      Rise      Tilt      Roll     Twist
*    1 GC/GC     -0.55      0.39      7.41      6.40     -4.22     23.36
     2 CG/CG     -0.05      0.87      2.44     -0.55      3.94     -0.81
*    3 GT/AC      0.38      0.47      7.23     -8.62      3.75     25.70
*    4 TA/TA     -0.00      4.73      3.09     -0.00      7.49     25.67
*    5 AC/GT     -0.38      0.47      7.23      8.62      3.75     25.70
     6 CG/CG      0.05      0.87      2.44      0.55      3.94     -0.82
*    7 GC/GC      0.55      0.39      7.41     -6.40     -4.22     23.36
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        ave.     -0.00      1.17      5.32     -0.00      2.06     17.45
        s.d.      0.39      1.59      2.50      6.21      4.49     12.52

The simple parameters are ‘intuitive’ for non-Watson-Crick base pairs and associated base-pair steps, where the existing standard-reference-frame-based 3DNA parameters may look weird. Note that these simple parameters are for structural description only, not to be fed into the ‘rebuild’ program. Overall, they complement the rigorous characterization of base-pair geometry, as demonstrated by the original analyze/rebuild pair of programs in 3DNA.

In short, the ‘simple’ base-pair parameters employ the YC6—RC8 vector as the y-axis whereas the ‘simple’ step parameters use consecutive C1’—C1’ vectors. As before, the z-axis is the average of two base normals, taking consideration of the M–N vs M+N base-pair classification. In essence, the ‘simple’ parameters make geometrical sense by introducing an ad hoc base-pair reference frame in each case. More details will be provided in a series of blog posts shortly.

Overall, this new section of ‘simple’ parameters should be taken as experimental. The output can be turned off by specifying the analyze -simple=false command-line option explicitly. As always, I greatly appreciate your feedback.

In DSSR (and find_pair -p from the original 3DNA suite), multiplets is defined as “three or more bases associated in a coplanar geometry via a network of hydrogen-bonding interactions. Multiplets are identified through inter-connected base pairs, filtered by pair-wise stacking interactions and vertical separations to ensure overall coplanarity.”

DSSR detects multiplets automatically, and outputs a corresponding MODEL/ENDMDL delineated PDB file (dssr-multiplets.pdb by default) where each multiplet is laid in the most extended view in terms of base planes. The DSSR Nucleic Acids Research (NAR) paper contains four examples (in supplemental Figures 1, 3, 4, and 7) to illustrate this functionality. Please refer to Reproducing results published in the DSSR-NAR paper on the 3DNA Forum for details.

Recently, I read the article titled InterRNA: a database of base interactions in RNA structures by Appasamy et al. in NAR. In Figure 2 (linked below) of the paper, the authors showcased a sextuple (hexaplet) identified in the E. coli ribosome (PDB id: 4tpe), along with six base-base H-bonds contained therein.

Figure 2. Example of the user interface displaying an InterRNA database record.

With interest, I tried to run DSSR on the PDB entry 4tpe. As it turns out, ‘4tpe’ has been merged into 4u27 in mmCIF format. I ran DSSR (v1.4.6-2015dec16) in its default settings on ‘4u27’ and get the following summary of results.

# x3dna-dssr -i=4u27.cif -o=4u27.out
    total number of base pairs: 4822
    total number of multiplets: 680
    total number of helices: 264
    total number of stems: 566
    total number of isolated WC/wobble pairs: 193
    total number of atom-base capping interactions: 615
    total number of hairpin loops: 215
    total number of bulges: 137
    total number of internal loops: 244
    total number of junctions: 108
    total number of non-loop single-stranded segments: 83
    total number of kissing loops: 14
    total number of A-minor (type I and II) motifs: 246
    total number of ribose zippers: 127
    total number of kink turns: 15

Among the 680 DSSR-identified multiplets, two hexaplets (one on chain “AA”, and another on “CA”) match those reported by Appasamy et al., as shown below:

 678 nts=6 GUUAAA 1:AA.G404,1:AA.U438,1:AA.U439,1:AA.A496,1:AA.A498,1:AA.A499
 679 nts=6 GUUAAA 1:CA.G404,1:CA.U438,1:CA.U439,1:CA.A496,1:CA.A498,1:CA.A499

For illustration, the hexaplet #678 is extracted from dssr-multiplets.pdb to file 4u27-hexaplet.pdb (download the coordinates) and shown below. The figure is generated by DSSR and PyMOL, as detailed in Reproducing results published in the DSSR-NAR paper on the 3DNA Forum.

x3dna-dssr -i=4u27-hexaplet.pdb -o=4u27-hexaplet.pml --hbfile-pymol 

DSSR-identified hexaplet GUUAAA in 4u27.

DSSR identifies 6 base pairs in the hexaplet:

# x3dna-dssr -i=4u27-hexaplet.pdb --idstr=short
List of 6 base pairs
      nt1            nt2           bp  name        Saenger    LW  DSSR
   1 G404           A498           G+A --          n/a       tSS  tm+m
   2 G404           A499           G+A --          n/a       cWH  cW+M
   3 U438           A496           U-A rHoogsteen  24-XXIV   tWH  tW-M
   4 U439           A496           U-A --          n/a       cH.  cM-.
   5 U439           A498           U-A WC          20-XX     cWW  cW-W
   6 A496           A498           A+A --          n/a       cWH  cW+M

It detects a total of 9 H-bonds as shown below. In addition to the 6 base-base H-bonds noted by Appasamy et al., DSSR also finds 3 sugar-base H-bonds (#1, #2, and #4, labeled in green) that obviously play a role in stabilizing the high-order base association.

# x3dna-dssr -i=4u27-hexaplet.pdb --get-hbonds --idstr=short
   11    59  #1     o    3.017 O:N O2'@G404 N3@U439
   11   104  #2     o    2.578 O:N O2'@G404 N1@A498
   18   125  #3     p    3.089 O:N O6@G404 N6@A499
   21    96  #4     o    3.289 N:O N2@G404 O2'@A498
   21   106  #5     p    2.797 N:N N2@G404 N3@A498
   39    78  #6     p    2.944 N:N N3@U438 N7@A496
   61    81  #7     p    3.167 O:N O4@U439 N6@A496
   61   103  #8     p    2.662 O:N O4@U439 N6@A498
   82   103  #9     p    3.152 N:N N1@A496 N6@A498

Over the years, I have played quite a few computer programming languages. ANSI C has become my top choice for ‘serious’ software projects, due to its small size, efficiency, flexibility, and ubiquitous support. Moreover, C is a mature language, with a rich ecosystem. As it turns out, C has also been consistently rated as one of the most popular computer languages (#1 or #2) over the past thirty years.

Needless to say, ANSI C has its own quirks, and it takes a steep learning curve. However, once you get over the hurdles, the language serves you. I cannot remember when, but it has been a long while that coding in ANSI C is no longer an issue. It is the understanding of scientific questions that takes most of my time, and coding helps greatly in refining my thoughts.

Not surprisingly, ANSI C was chosen as the sole language for DSSR (and SNAP, or 3DNA in general). The ensure the overall quality of the DSSR codebase, I have taken the following steps:

• The whole project is under git.
• The ANSI C source code is compiled with strict GCC options for full compliance to the standard:

-ansi -pedantic -W -Wall -Wextra -Wunused -Wshadow -Werror -O3

• The executable is checked with valgrind for any memory leak:

valgrind --leak-check=full x3dna-dssr -i=1ehz.pdb -o=1ehz.out --quiet
==19624== Memcheck, a memory error detector
==19624== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==19624== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info
==19624== Command: x3dna-dssr -i=1ehz.pdb -o=1ehz.out --quiet
==19624==
==19624==
==19624== HEAP SUMMARY:
==19624==     in use at exit: 0 bytes in 0 blocks
==19624==   total heap usage: 52,829 allocs, 52,829 frees, 92,878,578 bytes allocated
==19624==
==19624== All heap blocks were freed -- no leaks are possible
==19624==
==19624== For counts of detected and suppressed errors, rerun with: -v
==19624== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

• Extensive tests (with the simple diff command) to ensure the program is working as expected.

The above four measures combined allow me to add new features, refactor the code, and fix bugs, without worrying about accidentally breaking existing functionality. Reading literature (including citations to 3DNA/DSSR) and responding to user feedback on the 3DNA Forum keep me continuously improve DSSR. Some of the recent refinements to DSSR came about this way.