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2
FAQs / How to set up 3DNA on Windows
« on: July 14, 2017, 12:44:23 pm »
3DNA v2.3 and before contain a suite of programs, and associated data files. Setting up 3DNA is intended to be a simple process for those with command-line experience: it entails creating an environment variable named X3DNA to point to where 3DNA is stored, and an updated PATH that includes the $X3DNA/bin directory. The whole process is facilitated by a Ruby script, x3dna_setup, and should take no more than a few minutes.

With Linux and Mac OS, setting up 3DNA has normally not be an issue. For Windows, however, the situation is more complicated than desired. Cygwin or MinGW/MSYS is the preferred way to run 3DNA on Windows, but each requires the installation of a big package and the ending environment is not familiar to Windows users. By far, the most frequent and longest threads on the Forum are on how to properly set up 3DNA on Windows, initiated by new users who have no experience in command-line interface.

As of 3DNA v2.3.1-2017jun24, the compiled .exe files in the tarball x3dna-v2.3-mingw-win.tar.gz should run in native Windows (i.e. without Cygwin or MinGW/MSYS) via the command prompt. However, the default Windows command prompt (cmd.exe) is a dinosaur and awkward to use. I played with Windows PowerShell a bit, but it gave some surprises with processing of command-line options. The win-bash shell may be a choice, or one can install Bash on Windows 10.

In the long run, when the 'Bash on Windows' becomes a default, the whole issue of setting 3DNA will on longer exist any more. In the meantime, this FAQ entry provides detailed instruction on how to set up 3DNA v2.3 on native Windows (tested on Windows 7).

  • Install ConEmu (Stable, Installer) -- it is far superior to Windows cmd.exe
    Quote
    ConEmu-Maximus5 is a Windows console emulator with tabs, which presents multiple consoles and simple GUI applications as one customizable GUI window with various features...file and archive management, command history and completion, powerful editor.

  • Download the Windows version of 3DNA v2.3, the x3dna-v2.3.zip file (Note that you need to register and log in to see the download link). The zip file normally ends up in the Downloads/ folder under your home folder (e.g., C:\Users\xiangjun\Downloads.)
  • Right-click the x3dna-v2.3.zip file, in the context menu select "Extract All...". In the setting window, you can select the folder under which 3DNA will be installed. Please do not specify x3dna-v2.3 explicitly in setting the folder, since x3dna-v2.3 will always be appended to it.

    In principle, you can install 3DNA anywhere. It is a good choice to put it directly under your home folder (e.g., C:\Users\xiangjun). See the screenshot below.



    Click the "Extract" button at the bottom right. You'll see lots of files being extracted. Take a note of the 3DNA folder (i.e., C:\Users\xiangjun\x3dna-v2.3\ as shown above) as this information is needed next.

    Navigate to the designated 3DNA folder and make sure it has the content shown below. Right-click on file license.txt and select "Properties". The Location: field should report its parent folder (no ending slash) that agrees with the one shown above.




  • Set the X3DNA environment variable and update the PATH. See "How to set the path and environment variables in Windows" for details. Here I am using Windows 7 as an example.

    • From the "Desktop", right-click the "Computer" icon and select "Properties". If you don't have a Computer icon on your desktop, click the "Start" button, right-click the "Computer" option in the Start Menu, and select "Properties".
    • Click the "Advanced System Settings" link in the left column.
    • In the System Properties window, click on the "Advanced" tab, then click the "Environment Variables..." button near the bottom of that tab.
    • In the Environment Variables window, the top part is for User variables (for xiangjun in the example). Click the "New..." button, and you will see the New User Variable window. For the Variable name text field, type X3DNA, and for Variable value, type C:\Users\xiangjun\x3dna-v2.3\ (with ending slash). Note that this value must match what is specified in the extraction step, i.e., pointing to where 3DNA is actually installed. See the following screenshot.



      Click the "OK" button, and the result is as shown below:

    • In the Environment Variables window, the bottom part is for System variables. Scroll to find the Path variable, which contains a long list of values separated by semicolon (e.g. C:\Windows\system32;...). Highlight (select) the Path entry and click the "Edit..." button. The Edit System Variable window will appear. The Variable name text field will be Path. Scroll to the end of Variable value, add ;C:\Users\xiangjun\x3dna-v2.3\bin. Note that each different directory is separated with a semicolon. See screenshot below.

  • Now double-click the ConEmu icon on the desktop to open a new terminal window. Type find_pair -h in the command prompt, you should see a result screen as shown below.


  • Optionally, install Ruby on Windows. You may skip this step when you just get started with 3DNA on Windows. The Ruby scripts distributed with 3DNA v2.3 are mostly for generating schematic block images, and analyzing NMR ensembles.

    Do not forget to click the check box "Add Ruby executables to your PATH". See the first entry in Troubleshooting.



    Note that at the end of the installation, you do not need to click the checkbox to install "MSYS2 and development toolchain". 3DNA v2.3 runs just fine as is, even though getting them installed does not hurt.

If you notice any problem, please post below with details.

3
The DSSR-Jmol paper, titled "DSSR-enhanced visualization of nucleic acid structures in Jmol", has been officially published in the 2017 web-server issue of Nucleic Acids Research (NAR). Notably, the work has been featured in the cover image, as shown below:

"Cover image featuring the DSSR-Jmol paper" title="Cover image featuring the DSSR-Jmol paper"

Quote
Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).

The DSSR-Jmol integration bridges the DSSR command-line analyzing tool and the Jmol molecular viewer seamlessly together via the standard JSON interface. Now users can select DSSR-derived RNA structural features (such as base pairs, double helices, various loops, etc.) and visualize them in novel representations in Jmol interactively. Moreover, fine-grained characteristics of these features can be queried via the Jmol SQL for DSSR. The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, and brings RNA visualization to an entirely new level. The web interface (http://jmol.x3dna.org) is fully functional and easy to use, serving a huge user base of researchers, educators, and students alike.

Featured as the cover image of the 2017 NAR web-server issue, DSSR's publicity would surely increase through the DSSR-Jmol integration. Additionally, I've written a new post (on the 3DNA Forum) that provides the scripts and datafiles used to create the cover image.

4
DSSR-Jmol integration / cover image
« on: June 30, 2017, 01:56:36 pm »
"Cover image featuring the DSSR-Jmol paper" title="Cover image featuring the DSSR-Jmol paper"

Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).


Upper left corner (Jmol script: 4fe5.scr; image: 4fe5.png):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk
frank off
write PNGJ 3000 3000 4fe5-raw.png


Upper middle (Jmol script: 1fjg.scr; image: 1fjg.png):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =1fjg/dssr
select nts; display nts
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer
frank off
write PNGJ 3000 3000 1fjg-raw.png


Upper right corner (Jmol script: 1ehz.scr; image: 1ehz.png):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =1ehz/dssr
select nts; display nts
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select hairpins; color red
select junctions; color blue
frank off
write PNGJ 3000 3000 1ehz-raw.png


Bottom (Jmol script: 5ktj.scr; image: 5ktj.png):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =5ktj/dssr
select nts; display nts
rotate best
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
frank off
write PNGJ 3000 3000 5ktj-raw.png



The 'raw' images were automatically generated from the corresponding script files via command line using the Jmol application with options -ions. The ImageMagick convert program was used to remove empty boundaries. Using 4fe5 as an example, the procedure is as follows:

Code: [Select]
jmol -ions 4fe5.scr   # generate 4fe5-raw.png
convert -trim +repage -border 10 -bordercolor white 4fe5-raw.png 4fe5.png

The four images were then combined using InkScape, and exported to one big composite PNG file (DSSR-Jmol-for-NAR17-web-cover.png, 18MB).


Finally, the tarball file, reproduce-dssr-jmol.tar.gz, contains all the scripts and data files for reproducing the cover image.

5
FAQs / How to make the best use of the Forum
« on: May 19, 2017, 11:35:45 am »
  • Register to download the 3DNA software (including DSSR and SNAP) and to post questions. Non-registered viewers can only read existing posts; they will not see the 'Downloads' section and they are not allowed to post on the Forum. Over the years, I've received many private emails asking for help, and have responded to most of those users with the following canned message:

    Quote
    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 about all 3DNA-related issues. In other words, *any* 3DNA-associated questions are welcome and should be directed there. Specifically, please do *not* be shy in sharing openly and concretely difficult experiences you may have in installing or using the software.

    By asking your questions on the public 3DNA Forum, you are not only benefiting yourself but also the user community. I monitor the Forum regularly and always respond to posts promptly. I look forward to 'seeing' you on the 3DNA Forum (http://forum.x3dna.org/).
  • Post on the Forum any 3DNA-related questions, or share your experience/use case with the community. After registration, you must post your questions yourself on the Forum to get them answered. I do not post questions asked privately via email on the Forum on your behalf.

    By posting your questions on the 3DNA Forum, you are asking for help from others, for free. Be appreciative if you receive responses. Be open minded, since your questions may not be answered in a way you expect, or receive any reply at all.

    Your posts on the 3DNA Forum are in the public domain. Search engines like Google index and cache the website. The 3DNA Forum is automatically backed up every day.
  • Click the Notify button (in the upper right corner) to receive email alerts for new posts in the threads or sections you are interested in. You can also change your settings for notifications and newsletters via "Profile" • "Modify Profile" • "Notifications" (login required).
  • Share what you know that could be of interest to the general 3DNA user community. Be helpful.
  • Behave yourself. No spam or trolling allowed. Violators are removed immediately without any further notice.
  • Remove your account. If you no longer need to access the 3DNA Forum, please login and then click: "Profile" • "Actions" • "Delete this account". You are responsible removing your own account. It is your choice to join, and it is your freedom to leave.

6
Site announcements / DSSR-Jmol paper in NAR
« on: May 05, 2017, 05:20:04 pm »
I am pleased to announce the (advance online, May 3, 2017) publication of a new paper titled ["DSSR-enhanced visualization of nucleic acid structures in Jmol"](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365) in *Nucleic Acids Research* (NAR). Co-authored by Robert Hanson (Jmol) and me (DSSR), the article will appear in the July 2017 web-server issue of NAR. Here are the key links related to the paper:

* [DSSR-Jmol website](http://jmol.x3dna.org/)
* [PDF version (DSSR-Jmol paper)](https://academic.oup.com/nar/article-pdf/doi/10.1093/nar/gkx365/14134996/gkx365.pdf)
* [Online HTML (DSSR-Jmol paper)](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365)
* [DSSR-Jmol manual](http://jmol.x3dna.org/dssr-jmol-manual.pdf)
* [Materials to reproduce reported results](http://forum.x3dna.org/dssr-jmol-integration/)

The DSSR-Jmol integration project was initiated in October 2013 when I approached Bob at a meeting organized by RCSB PDB at Rutgers. Thereafter, we met only once in July 2014 in Paris. Over the years, we have mostly communicated via email, occasionally facilitated by Skype. Our work bridges the DSSR command-line analyzing tool and the Jmol molecular viewer together via a simple JSON interface and a powerful query language. Users can now select DSSR-derived RNA structural features (such as base pairs, double helices, and various loops) as easily as they can select protein alpha-helices and beta-strands. Moreover, fine-grained characteristics of these features can be queried via Jmol SQL for DSSR (see examples below). Notably, the novel representation styles (step diagram and base blocks) and coloring schemes bring RNA visualization to an entirely new level (see [Figure 3 of the paper](http://forum.x3dna.org/dssr-jmol-integration/figure-3)).

Code: Bash
  1.     load =1ehz/dssr   # load yeast phenylalanine tRNA to Jmol with DSSR annotation
  2.     SELECT hairpins   # select the three hairpin loops
  3.     SELECT junctions  # select the four-way junction loop
  4.     select within(dssr, "nts WHERE is_modified")  # select modified nucleotides (14 total)
  5.     SELECT within(dssr, "pairs WHERE name != 'WC'")  # select non-Watson-Crick pairs
  6.     SELECT within(dssr, "pairs WHERE name = 'WC' OR name = 'Wobble'")  # select canonical pairs
  7.     Select within(dssr, "pairs WHERE name != 'WC' AND name != 'Wobble'")  # select non-canonical pairs
  8.     SELECT within(dssr, "pairs WHERE LW = 'tSW'")  # select pairs of type tSW per Leontis-Westhof

The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, serving a huge user base of researchers, educators, and students alike. Its functionality is freely accessible either via the **Jmol application**, or the **JSmol-based website** (http://jmol.x3dna.org). By adhering to web standards, the website is fully functional in all modern browsers on various computer/operating systems (including handheld devices, such as tablets and smart phones). The web interface is simple and intuitive, and new users can get started easily. It also allows power users to take full advantage of Jmol scripting via a command-line console.

This work also provides an example for integrating DSSR-derived features into other molecular graphics programs or bioinformatics pipelines involving nucleic acid structures. By design, DSSR is a stand-alone, command-line program written in ANSI C. The binary executables are only ~1MB in size, and *self-contained*. With zero dependencies, no setup or configuration, it is trivial to get DSSR up and running. DSSR uncovers a wide range of RNA/DNA structural features in a consistent, easily accessible framework. It possesses a much richer set of functionalities for nucleic acid structural analysis (see the [DSSR User Manual](http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf)) than any other existing tools I am aware of. Moreover, the program is efficient and robust, making it an ideal component to be integrated into other pipelines, especially via the standard and structured **JSON** interface.

Collaborating with Bob has been a truly exciting experience. The NAR-web publication represents a gratifying intermediate result along an on-going journey. Hopefully, others (may be some of you) can join us in pushing forward the field of RNA structural bioinformatics.

Best regards,

Xiang-Jun

7
DSSR-Jmol integration / Figure 3
« on: May 04, 2017, 02:06:12 pm »
"Sample molecular images enabled by the DSSR-Jmol integration" title="Sample molecular images enabled by the DSSR-Jmol integration"

Figure 3. Sample molecular images illustrating selected RNA structural features enabled by the DSSR-Jmol integration. (A) Structure of yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram with bases labeled, highlighting (in red) the [2,1,5,0] four-way junction loop in 3D. (B) Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the vertical helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions. (C) Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red. (D) Structure of the yeast GAL4 protein-DNA complex (PDB id: 1d66) in Jmol cartoon representation. DNA is color-coded by DSSR stems, and protein is in translucent brown. The DNA helix is broken into two stems due to a non-Watson-Crick pair (G11 with C28 in gray) in the middle. (E) Structure of the Thermus thermophilus 30S ribosomal subunit in complex with the antibiotics (PDB id: 1fjg) using a step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5'-end in blue and the 3'-end in red.


Figure 3A (Jmol script: 1ehz.scr):
Code: [Select]
load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
set fontSize 4
background white; color grey
select nucleic and leadAtom; spacefill 1.5
label %[group1]; set labeloffset 0 0; color labels yellow
select junctions; color red
select selected and *.P; label %n%r; color label black; set labeloffset 0 0; set labelfront;
select @{_M.dssr.nts.select("where is_modified")} and *.P; color label blue


Figure 3B (Jmol script: 5ktj.scr):
Code: [Select]
load =5ktj/dssr
cartoon only
select nts; display nts
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
rotate best; rotate z -90; rotate y 90


Figure 3C (Jmol script: 4ef5.scr):
Code: [Select]
load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk


Figure 3D (Jmol script: 1d66.scr):
Code: [Select]
load =1d66/dssr
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
color property DSSR stems
select protein; color TRANSLUCENT 0.9 brown


Figure 3E (Jmol script: 1fjg.scr):
Code: [Select]
load 1fjg.pdb
calculate structure dssr
cartoon only
select nts; display nts
rotate best
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer

8
DSSR-Jmol integration / Table 1
« on: May 04, 2017, 01:45:06 pm »
Here is Table 1 and the corresponding DSSR/jq command for each example item on the right column [other than "Jmol (SQL) selections"].

Table 1. DSSR-derived features and DSSR-specific selections in Jmol, using yeast phenylalanine tRNA (1ehz) as an example

Code: Javascript
  1. Accessible features (16 keys)  ["pairs","multiplets","helices","stems","isoCanonPairs","coaxStacks","hairpins","bulges","iloops","junctions","kissingLoops","ssSegments","stacks","nonStack","hbonds","nts"]
  2.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.paths | keys_unsorted'
  3.  
  4. Actual counts (1ehz)           {"pairs":34,"multiplets":4,"helices":2,"stems":4,"isoCanonPairs":1,"coaxStacks":2,"hairpins":3,"junctions":1,"kissingLoops":1,"ssSegments":1,"stacks":11,"nonStack":4,"hbonds":118,"nts":76}
  5.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .counts
  6.                                
  7. Base pair (G1–C72)             {"index":1,"nt1":"|1|A|G|1||||","nt2":"|1|A|C|72||||","bp":"G-C","name":"WC","Saenger":"19-XIX","LW":"cWW","DSSR":"cW-W"}
  8.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .pairs[0]
  9.                                
  10. Nucleotide (2MG10)             {"nt_name":"2MG","nt_id":"|1|A|2MG|10||||","is_modified":true,"chi":169.599,"puckering":"C3'-endo"}
  11.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.nts[9] | {nt_name, nt_id, is_modified, chi, puckering}'
  12.  
  13. Jmol (SQL) selections          SELECT hairpins
  14.                                SELECT within(dssr, "nts WHERE is_modified")
  15.                                SELECT within(dssr, "pairs WHERE name !='WC'")
  16.  

9
DSSR-Jmol integration / The graphical abstract
« on: May 04, 2017, 01:35:32 pm »
"DSSR-enhanced visualization of tRNA (1ehz)" title="DSSR-enabled visualization of tRNA (1ehz)"

3D interactive visualization of the classic L-shaped tRNA (PDB id: 1ehz) with the three hairpin loops highlighted in red and the four-way junction loop in blue. The image was created using the DSSR-Jmol integration.



The Jmol script (abstract-graphics.scr) used to create the original image is shown below. The image was annotated using Inkscape.

Code: [Select]
# Jmol 14.13.1 (2017-04-09)
load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select hairpins; color red
select junctions; color blue

The raw image from the above script is as below:

"DSSR-enhanced visualization of tRNA (1ehz)" title="DSSR-enabled visualization of tRNA (1ehz)"

10
I am excited to announce that a paper titled "DSSR-enhanced visualization of nucleic acid structures in Jmol" has just been published online for the 2017 web-server issue of Nucleic Acids Research (NAR). Co-authored by Robert Hanson and me, this paper represents an idealized result I could expect from a scientific collaboration. I first approached Bob in October 2013 at a meeting organized by RCSB PDB at Rutgers, and we then met again in July 2014 in Paris. Over the years, we have communicated extensively via email, facilitated by Skype. Collaborating with Bob has been a truly exciting experience, and it is gratifying to see a joint publication coming out of our efforts.

The DSSR-Jmol integration bridges the DSSR command-line analyzing tool and the Jmol molecular viewer seamlessly together via a simple JSON interface and a powerful query language. This work fills a gap in RNA structural bioinformatics, and brings the 3D interactive visualization of nucleic acid structures to an entirely new level. The website (http://jmol.x3dna.org) is fully functional, useful to researchers, educators, and students alike. Furthermore, it can serve as a starting point for anyone who wishes to develop additional interactive web-based resources involving nucleic acid structures.

The DSSR-Jmol paper has been featured in the cover image of the NAR'17 web-server issue. Undoubtedly, this recognition would further increase this publicity of this solid piece of work. (note added on June 30, 2017)

The abstract of the paper is quoted below:

Quote
Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org).

This section on the 3DNA Forum is dedicated to topics on reproducing the results reported in the DSSR-Jmol article, and the cover image. Scripts and related data files where necessary are provided so interested parties can rigorously reproduce our results. We welcome any questions and comments you may have. Please post them here instead of (or in addition to) sending me emails.





Note that the reported results in the paper were based on DSSR version 1.6.8 (released on 2017-03-28) and Jmol version 14.13.1 (released on 2017-04-09). During the proof stage, Jmol was updated to version 14.15.1 (released on 2017-04-27), which was the one reported in the manuscript and the supplementary data.

Best regards,

Xiang-Jun




For completeness, here are Figure 1 (brief description of DSSR algorithms) and Figure 2 (screenshot of the DSSR-Jmol website).

"Definitions of key nucleic acid structural components in DSSR" title="Definitions of key nucleic acid structural components in DSSR"

Definitions of key nucleic acid structural components in DSSR [reproduced from Figure 1 of reference (9)]. (A) Nucleotides are recognized using standard atom names and base planarity. This method works for both the standard bases (A, C, G, T and U), and those of modified nucleotides, regardless of their tautomeric or protonation states. (B) Bases are assigned a standard reference frame (25) that is independent of sequence identity: purines and pyrimidines are symmetrically placed with respect to the sugar. (C) The standard base frame is derived from an idealized Watson-Crick base pair, and defines three base edges (Watson-Crick, minor groove, and Major groove) that are used to classify pairing interactions. (D) Base pairs are identified from the co-planarity of base rings and the occurrence of hydrogen bonds. This geometric algorithm can find canonical (Watson-Crick and G–U wobble) as well as non-canonical pairs. Higher-order (three or more) co-planar base associations, termed multiplets, are also detected. (E) Helices are defined by stacking interactions of base pairs, regardless of pairing type (canonical or otherwise) or backbone connectivity (covalently connected or broken). A helix consists of at least two base pairs. The same algorithm is applied to identify continuous base stacks that are outside of helical regions, by using bases instead of pairs as the assembly unit. Nucleotides not involved in base-stacking interactions are collected into one separate group. A stem is defined as a special type of helix, made up of canonical pairs and with a continuous backbone along each strand. Coaxial stacking is defined by the presence of two or more stems within one helix. An isolated canonical pair is one that is not contained within a stem. (F) ‘Closed’ loops of various types (hairpin, bulge, internal, and junction loops) are delineated by stems or isolated pairs, and specified by the lengths of the intervening, consecutive nucleotide segments. A kissing-loop motif entails formation of one or more canonical pairs between the bases in different hairpin loops. Single-stranded segments that lie outside loops are separately listed.


"Screenshot of the DSSR-JSmol web interface" title="Screenshot of the DSSR-JSmol web interface"

A screenshot of the DSSR-JSmol web interface, highlighting the two reverse Hoogsteen pairs (U8–A14 and 5MU54–1MA58) of yeast phenylalanine tRNA (PDB id: 1ehz). (A) DSSR-derived structural features integrated into Jmol. (B) The main JSmol viewer canvas for visualization and interactive manipulations. (C) Common representation styles for selected structural features. (D) A simple text input field for advanced users to enter (short) Jmol script commands. (E) Structure input by PDB id, file upload (drag-and-drop), or selecting one from the twelve sample RNA structures. (F) Utilities to toggle between two states for six common cases. (G) Export of coordinate file or PNG image. (H) Links to online resources for DSSR and Jmol.

11
Site announcements / Highlights of recent developments of 3DNA/DSSR
« on: November 20, 2016, 07:13:58 pm »
Dear 3DNA Forum subscribers,

Here are some highlights of recent developments of 3DNA/DSSR:

Note: If you've difficulty in accessing the 3DNA homepage, possibly the case from mainland China (as I know it), please visit its duplicate at http://home.x3dna.org. This newsletter is written in Markdown, with a translated HTML version posted on the 3DNA homepage.

3DNA v2.3
  • The C source code is now available. Since the programs are written in strict ANSI C, 3DNA can be compiled (as is) on any computers/operating systems with a C (or C++) compiler. For user convenience, three binary distributions (with source code under the src/ subdirectory) are provided for Windows, Linux, and Mac OS X. The distributed Windows version works in native Windows (7 and up, via the cmd command-line interface, or ConEMU), MinGW/Msys (Msys2), and Cygwin, in either 32 or 64-bit.
  • A new set of 'simple' base-pair and step parameters was introduced to give 'intuitive' numerical values for non-Watson-Crick base pairs and associated steps. See the short communication titled Characterization of base pair geometry in the January 2016 issue of Computational Crystallography Newsletter (CCN).
  • The fiber program includes a new option, --pauling, for easy generation of Pauling & Corey triplex models of DNA/RNA with arbitrary base sequence. See my blogpost titled Pauling's triplex model of nucleic acids is available in 3DNA.
  • Thomas Holder (PyMOL Principal Developer at Schrödinger, Inc.) has built a PyMOL wrapper to 3DNA fiber models. Now generating standard, regular DNA/RNA models in PyMOL is straightforward -- thanks, Thomas!

DSSR (Dissecting the Spatial Structure of RNA)
  • Selected features of DSSR have been incorporated into Jmol (in collaboration with Robert Hanson, Jmol Principal Developer), and PyMOL (in collaboration with Thomas Holder). In Jmol application (via the Console window), one can now, for example, load =1ehz/dssr and then select hairpins; color red to see where the three hairpin loops are in 3D. The Jmol-DSSR web interface makes DSSR-enhanced visualization of nucleic acid structures in Jmol readily accessible to a broad user base, and has been employed in classes for educational purpose. A sample image of DSSR-derived cartoon-block representation via PyMOL is available for PDB entry 5dww, which has a G-quadruplex-duplex interface.
  • Since the publication of the Nucleic Acids Research paper in 2015, DSSR has been continuously refined and expanded, with a total of 36 new releases (from v1.2.8 to v1.6.4) as of this writing. Notably, the --json option provides DSSR-derived parameters in the simple, structured, and standard JSON format that can be easily parsed. This JSON output format is the (preferred) way for the outside world to interface with DSSR, and the Jmol-DSSR integration is built upon it. The --nmr option allows for batch processing of MODEL/ENDMDL-delineated NMR ensembles or trajectories of molecular dynamics (MD) simulations. Did you know that scripts and data files for reproducing the reported results are available in the DSSR-NAR paper section on the 3DNA Forum?
  • The User Manual is now 88-page long, covering nevertheless only the most common use cases of what DSSR has to offer. Miss a feature that you would like to have? Maybe it is already there or can be easily implemented in DSSR. Simply ask (on the 3DNA Forum), and I'll try my best to help.

SNAP (Structures of Nucleic Acid-Protein complexes)
  • SNAP aims to consolidate, refine, and significantly extend commonly used functionalities for DNA/RNA-protein structural analysis in one easy-to-use program. Currently in beta testing, SNAP is already fully functional, with features for characterizing the protein-nucleic acid interface and identifying amino acid-base pairing and stacking interactions.

A note for 3DNA/DSSR users in mainland China: It's a pleasure to see the ~100 registrations on the 3DNA Forum with emails ending in .cn, 163.com, or qq.com etc., mostly from recent years. I'm planning a trip to China in 2017, and I'd be happy to meet some of you for academic exchanges and possible collaborations (学术交流、合作). If you're interested, let's get in touch!

Best regards,

Xiang-Jun

12
Site announcements / Pauling's triplex model of DNA and RNA
« on: November 17, 2016, 11:26:31 am »
As of v2.3-2016nov16, the 3DNA fiber program has added the --pauling option. This new feature is intended for easy generation of DNA/RNA triplex models based on the historical paper of Pauling and Corey in 1953, titled "A proposed structure for the nucleic acids". Combined with the existing --sequence option, 3DNA users can now construct a Pauling triplex model with arbitrary base sequence.

The basic usage is very straightforward, as illustrated in the following list of examples. There are also other variants as well, which may be useful for advanced users.

Code: [Select]
fiber -pauling triplex-C10C10C10.pdb        # default: 10 Cs per strand
fiber -pauling -seq=AAA triplex-A3A3A3.pdb  # 3 As per strand
fiber -pauling -seq=AAAA:CCCC:GGGG Pauling-triplex-A4C4G4.pdb
fiber -pauling -seq=ACGGUU,UUGGAC,GGAACC  Pauling-triplex-mixed.pdb
fiber --pauling-dna -seq=ACGGTT,TTGGAC,GGAACC  Pauling-triplex-DNA.pdb

A sample 3D image for the mixed sequence (last one in the above list, Pauling-triplex-DNA.pdb) is shown below:



See my blogpost titled "Pauling's triplex model of nucleic acids is available in 3DNA" for further information.

13
Site announcements / The number registrations has reached 3000
« on: October 15, 2016, 11:51:55 am »
As of October 15, 2016, the number of registrations on the 3DNA Forum has reached over 3,000! It takes slightly longer (15 days) than I predicted in my previous post "Summary of registrations" dated April 26, 2016, where I said:

Quote
If the current trend continues, the number of 3DNA Forum registered users will reach 3,000 by the end of September 2016.

In the past fews months, the number of new registrations has been in the 40s, slightly lower than the 50s averaged over previous years/months.

With 3,000 registrations from users all overall the world, yet no spams, the Forum is certainly functioning better than I could originally imagine. It serves well as a virtual platform that I can interact effectively with the ever-increasing 3DNA/DSSR user community. It is worth noting that the Forum has recently received contributions from Dr. Steve Harvey, a well-known computational structural biologist.

I'll write another announcement post when the number of registration reaches 5,000.

15
MD simulations / MOVED: Concatenated Helices
« on: August 29, 2016, 12:19:08 pm »

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.