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Messages - xiangjun

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1
General discussions (Q&As) / Re: build a DNA triangle for Gromacs
« on: April 17, 2018, 11:43:22 pm »
Hi Luxuan,

Thanks for your interested in using 3DNA and for posting your questions on the 3DNA Forum. Is your DNA triangle a planar structure? Is it equilateral? What the length of each side? Are the three sides connected?

There may be tools (e.g., "AMBER NAB") that better fit your needs. 3DNA does not provide a command to directly construct such a DNA triangle. Nevertheless, 3DNA has some low-level facilities for applications like this. For examples, you could use the fiber command to build three straight helices (in B-or A-form DNA) of selected sequence. Using analyze, you can locate the positions of a regular helix. Combined with case-specific geometric operations, 3DNA may help lead to a bottom-up approach that is reproducible via a script.

Check "build dna bulges and extend dna duplex at both terminals via 3dna" and search the Forum for more applications.

Xiang-Jun

2
Thanks for posting a DSSR-related question on the 3DNA Forum, and for correcting the link to the CompAnnotate paper. I became aware of this work shortly after its publication, and believe it is a useful resource in RNA structural bioinformatics.

As a meta-analysis tool, CompAnnotate takes advantage of other tools (including DSSR) in the initial identification of base-pairs, as noted below:

Quote
"Annotated base-pairing lists from the existing methods (MC-Annotate, RNAView, FR3D, DSSR and ClaRNA) are used as input for CompAnnotate and the corresponding modified base-pairing lists come as output."

To better appreciate the difference between DSSR and CompAnnotate, take a look of another tool "WebSTAR3D: a web server for RNA 3D structural alignment" developed by the same group. In the WebSTAR3D paper, the authors wrote:

Quote
Before aligning structures, STAR3D preprocesses PDB files with base-pairing annotation using either MC-Annotate (Gendron et al., 2001; Lemieux and Major, 2002) (for PDB inputs) or DSSR (Lu et al., 2015) (for PDB and mmCIF inputs) and pseudo-knot removal using RemovePseudoknots (Smit et al., 2008).

It is worth noting the following update on the WebSTAR3D website (see the attached screenshot),

Quote
Update 7/11/2017: WebSTAR3D no longer employs MC-Annotate for base pairing annotation.

Further down the webpage, it is noted "Before aligning structures, WebSTAR3D preprocesses PDBs with base pairing annotation using DSSR". So now DSSR is the only choice left for base-pair annotation.

As documented in the User Manual, DSSR has many more features to offer than just identifying and annotating base pairs. In case users have any questions, the 3DNA Forum is the way to go.

Hope this clarifies some of your confusions.

Xiang-Jun

3
Ths link you gave is invalid. Could you fix it?

Xiang-Jun

4
RNA structures (DSSR) / Re: Centre of Mass Pseudodihedral Angle
« on: April 03, 2018, 11:29:30 am »
Thanks for your followup. Now I can understand your original question a bit better. So COM stands for "center of mass" based on the attached figure caption. I still do not know what "CPD" stands for.

From the attached figure, it is still not clear to me what the two sugars above the target base are. Do the corresponding bases (attached to the sugars) must form a Watson-Crick (WC) pair? Do the three nucleotides where the base is in the middle must be consecutive in sequence?

Based on my understanding, I do not think adding this pseudo torsion angle (θ) is a good fit for DSSR (at least at this stage). See my post titled "Request for new features".

Why not ask for help from the author who defined this parameter? If that does not work out, you may write your own code or hire someone with basic programming skills for this purpose. Assuming the structure is a double helix with WC pairs, it should not be a big deal.

Xiang-Jun

5
RNA structures (DSSR) / Re: Centre of Mass Pseudodihedral Angle
« on: April 03, 2018, 08:33:33 am »
Hi,

Could you please let us know what exactly is “CPD (Centre of Mass Pseudodihedral Angle)”? Please also provide worked example so I can understand how to calculate it from atmoic coordinates.

Thanks,

Xiang-Jun

6
Howtos / Re: Mac OSX Compilation Difficulty
« on: April 02, 2018, 03:43:08 pm »
Thanks for chiming in regarding 3DNA installation in tcsh shell on macOS. The more such user feedbacks, the better.

Best regards,

Xiang-Jun

7
Hi Miriam,

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

I've a quick look of PDB entry 1ZRC, and found the following:

Quote
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.54(1.65)

The structure as a whole is curved to fit a sensible linear helical axis, as noted in the $X3DNA/config/misc_3dna.par:

Quote
# Section 4: is this double helix curved?
#   criterion to decide if a helix is strongly curved.
#   if relatively straight, 'analyze' will output a set of
#   global parameters, the normalized axis vector, and the
#   two end points the helical axis passes through
<std_curved>0.6</std_curved>

To calculate a bending angle, you need to divide the DNA into two fragments, each relatively straight. See also FAQ How to calculate DNA bending angle?

You may also want to give Curves+ a try. It is frequently used for quantifying DNA curvature in literature.

HTH,

Xiang-Jun

8
As a followup, DSSR v1.7.6-2018mar22 is released. The "--parallel" option is gone and the "--auxfile=no" is documented in the manual. The log-file is no longer generated by default.

Xiang-Jun

9
Thanks for the follow-up, which makes your point clearer. Let's proceed step-by-step.

Quote
1-I need to visualize triplex DNA via 3DNA.
   Explanation:3DNA is a software tool for the visualization of 3-dimensional nucleic acid structures. My designed DNA sequence (5'-AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC-3') was single strand and could form triple helix via Waston-Crick hydrogen bond and Hoogsteen hydrogen bond. The base pair is shown as follow. In the Figure, the round dots represent Waston-Crick hydrogen and the square dots represents the Hoogsteen hydrogen bond.

Based on your attached image, you could use the 3DNA fiber program to build the triplex part, as a starting point. Type fiber -m for available models (especially model #31 (or #30)). That's what the citation you referred to was talking about (as I understand).

See the 3DNA 2003 NAR paper, especially the section titled "MODEL BUILDING". In the 2008 3DNA Nature Protocols paper, pay attention to Box 6:

Quote
BOX 6 | FIBER-DIFFRACTION MODELS
The fiber program within 3DNA provides handy access to 55 fiber models of DNA and RNA helices in various polymorphic forms (e.g., A-, B-, C-DNA and so on) and stoichiometries (e.g., single-stranded, double-stranded, triplexes, quadruplexes and DNA–RNA hybrids). The program generates structure files in standard PDB format, with the ‘-xml’ option allowing for structural output in the new Protein Data Bank Markup Language72, a format especially useful for very large structures that exceed the five-digit atom serial number limit and/or the fixed (f8.3) Cartesian-coordinate formatting limit of PDB files. To the best of our knowledge, the collection of fiber models in 3DNA is the most comprehensive of its kind. In preparing this set of fiber models, we have taken great care to ensure the accuracy and consistency of the models. For completeness and user verification, 3DNA includes, in addition to 3DNA-processed files, the original coordinates collected from the literature. Whereas the 3DNA-processed repeating unit is necessary to construct full, atomic-level representations of the models, the structurally equivalent PDB files of the repeating units, expressed in standard base reference frame, prove useful as building blocks when a user wishes to generate a perturbed base-only fiber model, such as an overstretched duplex with variable rise at successive steps.

If you want to proceed with 3DNA, please become familiar with the 3DNA fiber command. Of course, you may well want to try some other modeling tools, such as NAB (Nucleic Acid Builder), or the many the start-of-the-art RNA modeling tools, as in the RNA-Puzzles game.

Xiang-Jun


10
Glad to hear your confirmation the suggested options did the trick.

In a future release of DSSR, the code/option for the log file will be revised (no x3dna-dssr.log file will be generated by default). I may also add an FAQ on running DSSR in parallel (as in GNU Parallel). Do not be surprised if the "--parallel" option is gone, or is replaced by another name with similar functionality. That's what an experimental option means, and why it is not documented.

Best regards,

Xiang-Jun


PS. Do not be shy in pointing out areas of DSSR that do not work as you expect (from a user's perspective). I'm always keen to improve DSSR in ways that make sense to me while incorporating users' feedback.

11
DSSR has many undocummented options. Even for the documented options, there are many undocumented variations thereof. As already mentioned several times in this Forum, there are two reasons: one is to keep the manual not too long, another is some featues are experimental (including using “--parallel”).

DSSR already has many documented features, probably far too many for a typical user would normally care. I’ve tried hard to ensure the accuracy of the documented features, and using this Forms as a means to promptly address users’ questions, and requests for ‘new’ functionality. Afterall, it is impossible to made DSSR (or any tool) perfectly fit to ever imaginable use case. As the author of DSSR, I’ve just made it work the way that makes sense to me, while listening carefully to users’ feedback.

Did the suggested options solve your problems?

Regards,

Xiang-Jun

12
Quote
Molecular Dynamics Simulations. The fiber module of the X3DNA program40 has been used to generate the PDB file template of the triple-helix model, exclusively formed by TAT sequence repetitions. The nucleotide sequence of the strands composing the triple helix has been modified through the X3DNA mutate_bases module40 in order to match the designed oligonucleotides sequences. ...

The above citation represents an expected use-case of the modeling features of the 3DNA suite of programs. Note that 3DNA is a software tool for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures. The description is clear, and should be simple to follow.

Quote
I need to visualize triplex DNA via 3DNA.

It is not clear to me what you mean here.

Quote
Firstly, the DNA sequence is designed by myself, which is AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC. I need your help to transform the sequences into PDB format. It is worth noting that the sequence is special for its self-complementary TAT and CGC triple base pair.

You are talking about a triplex DNA, which should have three strands. From the above description, I am not sure how the sequence is divided into three segments for the triplex. Please clarify.

Quote
And then, could you show me how to operate command line to generate PDB format using my own sequence?

The answer should become clear once the above steps are followed.

Best regards,

Xiang-Jun

13
Hi Justas,

Thanks for reporting the issue when running DSSR in parallel. Please try the following DSSR options in your script, and report back it does the trick.

Code: [Select]
--auxfile=no --parallel
Best regards,

Xiang-Jun

14
DNA-protein interactions (SNAP) / Re: Implement Json
« on: March 14, 2018, 02:28:42 pm »
Hi Honglue,

I've planned to add JSON output for SNAP when it reaches v1.0. Now you are interested in JSON output for "the staking [sic] interaction between nucleic acid base and amino acid side chain using SNAP". I was asking you for more details on the format of this part so I can tailor my effort to your specific need. What SNAP text output you want to be in JSON format? Please use a concrete example to make your point unambiguous.

Quote
Does that mean SNAP cannot output nucleic acid backbone interaction (only nucleic acid base)?

Please start a new thread. Again, using a concrete example so I can better understand what you mean.

Quote
I am currently training an undergraduate to analyze the interaction mode of RNA and protein. We will do the analyze for all the deposited protein RNA structures in RCSB.

You may want to try other available (and published) tools for analyzing RNA-protein interactions from PDB coordinates. SNAP is in beta testing version, after all.

Xiang-Jun

15
DNA-protein interactions (SNAP) / Re: Implement Json
« on: March 10, 2018, 10:59:32 pm »
I could add this portion in JSON for you to try out, if you (1) let me know more details on the format, and (2) agree to provide me with feedback on how the SNAP algorithm is working.

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.