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Messages - xiangjun

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1
General discussions (Q&As) / Re: blocview.pl
« on: September 30, 2020, 10:25:32 pm »
Within the 3DNA v2.4 distribution, the original Perl blocview script has been removed to avoid conflict with the Ruby script with the same name. The Ruby blocview script is the one to be used within 3DNA v2.0. Since you asked for the long outdated Perl script (no longer supported), I have dug it out -- see the attached file blocview.pl.

Note that DSSR 2.0 has replaced 3DNA v2.4. Specifically, the DSSR --blocview option has completely superseded the functionality of the Ruby blocview script in 3DNA v2.4, plus more advanced features. See the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" and http://skmatic.x3dna.org.

Best regards,

Xiang-Jun

2
Hi,

Thanks for your followup -- it helps clarify previous ambiguities.

In 3DNA, you could perform base mutations without changing backbone geometry using the mutate_bases program. As an example, to mutate U6 to DT, you can do the following:

Code: [Select]
mutate_bases 'chain=A snum=6 m=DT' rna2.pdb mutated-U6DT.pdb
You may mutate all four bases simultaneously. Check mutate_bases -h. You then need to remove O2' atoms manually.

DSSR 2.0 has a much powerful modeling module that supersedes mutate_bases, with many more features.

HTH,

Xiang-Jun


3
Please be specific: provide an example so that others can reproduce.

As a reminder, here is a list of items in the "Registration Agreement":

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

0.  Do your homework; read the FAQ and browse the Forum.
1.  Ask your questions on the *public* 3DNA Forum instead of sending
        xiangjun emails or personal messages. Additionally, please note
        that your posts on the 3DNA Forum are in the *public domain*.
2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.
3.  Respond to requests for clarification. Failure to do so may result in
        delay or no answer to your questions.
4.  Summarize the solution to your problem from a user's perspective
        by providing step-by-step details, for the community's benefit.
5+ Contribute back to the 3DNA project:
        o Report bugs — including typos
        o Make constructive suggestions — anything that can make 3DNA better
        o Answer other users' questions
        o Share your use cases in the "Users' contributions" section

Xiang-Jun

4
MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA
« on: September 16, 2020, 10:38:01 am »
Hi Moi,

Thanks for sharing your way of applying DSSR to the analysis of MD trajectories. The protocol you described is exactly a DSSR user-case I have in mind. DSSR is not targeted specially for MD simulations, for sure. Yet, DSSR fits pragmatically in most situations involving DNA/RNA structural bioinformatics, by design. The MD community will realize the simplicity and applicability of DSSR: it is just a timing issue (when, but not if).

Quote
Meanwhile, I notice that, when numbering the stems, I guess the program number the stems by their residue number (from 5' to 3'), namely, the helix with smaller resid at 5' side will be numbered first... Is this correct?

Yes. Try DSSR on 1ehz or other examples you are sure of to check this out.

Xiang-Jun

5
RNA structures (DSSR) / Re: Do you provide DSSR 1.* downloads ?
« on: September 15, 2020, 09:39:25 am »
Hi Louis,

Thanks for your inquires on the DSSR 2.0 release and the CTV licensing.

Only the latest DSSR is maintained to make the long-term support of the software simple and sustainable. DSSR 2.0 (and future releases) should be backward compatible: the main new features of DSSR 2.0 are the modeling modules and the professional manual. All DSSR-related issues should be reported on the open 3DNA Forum, unless a support agreement is arranged otherwise.

I have recently received quite a few enquires about the licensing terms on distributing DSSR as part of a pipeline or in a web service/server. CTV is woking on a policy on such usages. Please ask the CTV for an update on DSSR 2.0 licensing.

Best regards,

Xiang-Jun

6
RNA structures (DSSR) / Re: How to detect very distorted base pair?
« on: September 13, 2020, 01:34:34 pm »
Hi Honglue,

By default, DSSR does not detect these two base pairs because it fails to identify any H-bond between corresponding bases in each pair. These are the cases where users need pay attention to.

For your own understanding and the benefit of other users, it helps that you create an image for each of these base pairs, marking the distances between presumably H-bonded atoms.

Best regards,

Xiang-Jun

7
MD simulations / Re: Unnatural base pair helical parameters
« on: September 10, 2020, 08:18:18 am »
Hi Shaikh,

Quote
Can we apply this method to gromacs trajectory or amber trajectory. Or can we use multiple pdb frames to calculate helical parameters.

Follow my previous response, you should be able to find the answers to these questions. For your own understanding and the benefit of other viewers, please post back what you find.

Best regards,

Xiang-Jun

8
MD simulations / Re: Unnatural base pair helical parameters
« on: September 09, 2020, 08:29:51 pm »
Dear Dr. Shaikh,

Based on the PDB files you attached, the 3DNA find_pair program is working as expected with the -p option.

Quote
Do let me know how to calculate base pair parameters including major and minor groove parameters. There was one example in your homepage, but its not working in my case.

You need to run find_pair without the -p option, and feed the base-pairs list to the analyze program, as shown below:

Code: Bash
  1. find_pair onesb_frame1.pdb pairs_list.txt
  2. analyze pairs_list.txt
  3. # or combined as below:
  4. find_pair onesb_frame1.pdb | analyze

You may want to read the 2008 3DNA Nature Protocols paper, and the 2013 JoVE paper. See also the previous thread "Failed Downloading MD Ruby Scripts of 3DNA". You may want to give DSSR 2.0 a try: see the Overview PDF.

Best regards,

Xiang-Jun


9
MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA
« on: September 07, 2020, 10:21:51 am »
Hi Zhengyue,

Quote
Thank you for the detailed information! I got the license from the university last week, and then tried to install and run DSSR.

Glad to hear that you have been able to download and run DSSR successfully.

Quote
Unluckily, I noticed from the manual that DSSR only support PDB and mmCIF format... while my MD trajectories are millisecond-level netCDF file...while my MD trajectories are millisecond-level netCDF file... If I convert the trajectory to PDB files, it would be over 30 GB... So I cannot continue with it.

As noted explicitly in the DSSR manual, it is a deliberate decision to support only the standard .pdb and .cif formats. I am not a practitioner of MD simulations. Presumably, any decent MD packages should have a way to convert its proprietary binary format to one of the two standard ones. Large converted file size (30GB in your case) is indeed a technical issue. DSSR may not be a straightforward solution to your case yet. If you find a solution elsewhere OR come up with one of your own, please post back so other viewers of the thread can benefit from your experience.

Quote
As for my motivation to use 3DNA, I started working on Holliday Junction (HJ, a kind of DNA structure with four strands forming two helices, and two of the strands are shared by the two helices) recently by computational methods. Usually, the HJ conformation can be described by directions of helices. I hope that I can use the definition in 3DNA to describe the helix vectors so that I can see how those confirmations were sampled during the simulation (I failed to deal with it with cpptraj). Also, I want to monitor the base-pair H-bond along the helices during the simulation. Although cpptraj can solve it but this work is quite tedious:(

So it seems that 3DNA/DSSR  does have something unique to offer. Could you provide a small, typical example file to illustrate unambiguously what you want to achieve using 3DNA manually, and how it it solved with cpptraj?

To me, file size is only a technical issue. If DSSR 2.0 can indeed offer features not (easily) available elsewhere, save MD practitioners large amount of time, THEN I'd like to come up with a practical SOLUTION. I need a compelling case to be made. Otherwise, what's the point, why bother?

Quote
I also read some literatures and 3DNA and Curves+ are the only methods mentioned by those authors...(

3DNA and Curves+ have complementary features. Specifically, Curves+ has more parameters for quantifying groove dimensions and helix curvatures, and better/integrated support for MD simulations than 3DNA. You may ask "those authors" how 3DNA and Curves+ were used in their cases. See my blogposts:

Best regards,

Xiang-Jun

10
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« on: September 07, 2020, 10:20:34 am »
Hi,

Thanks for your interest in using DSSR 2.0, and for posting the questions on the 3DNA Forum. Without details, however, I cannot offer further help.

DSSR v2.0 is licensed by Columbia University, and it is only available from the Columbia Technology Ventures (CTV) website. From what I heard, the CTV has been responsive to legitimate requests for the three types of DSSR licenses.

Best regards,

Xiang-Jun

11
MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA
« on: September 04, 2020, 10:43:54 am »
Hi Moi,

Quote
Considering the microsecond-level AMBER trajectories and the situation of 3DNA, I finally asked the license of DSSR. I am still waiting for their response:)

Yes, DSSR 2.0 is the way to go. See the overview PDF.

Please let me know if you still do not hear back from CTV by early next week.

Quote
Hopefully, DSSR can solve my problem, I would like to try it and then have feedback here.

I am curious to know why do you want to use 3DNA/DSSR for the analysis of MD trajectories? Aren't there already dedicated tools (e.g., AMBER: CPPTRAJ) that *should* do the job, conveniently? In other words, what are still missing in those ready-to-use tools? I may be interested in extending MD analysis features in DSSR 2.0, ONLY IF justified by real-world applications.

Best regards,

Xiang-Jun


12
MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA
« on: September 02, 2020, 12:15:15 pm »
Hi Moi,

Quote
I am new to 3DNA and would like to use 3DNA for my MD trajectory analysis. So far, I have installed the standard 3DNA v2.4 and know that MD Ruby scripts and do_x3dna are two options for me.

Thanks for your interest in using 3DNA and for posting on the 3DNA Forum. The Ruby scripts distributed with 3DNA v2.4 may be appropriate for the analysis of an NMR ensemble in the PDB or short snapshot of MD trajectory. Check $X3DNA/bin/x3dna_ensemble script and $X3DNA/examples/ensemble.

"do_x3dna" is a third-party tool based on 3DNA. As far as I know, the "do_x3dna" project is no longer supported. Search the 3DNA Forum may give you some info.

Quote
However, I got a problem on entering  http://3dna.rutgers.edu:8080/data/x3dna_md_v0.1.tar.gz website. The browser said "this site cannot be reached". I further tested 3dna.rutgers.edu website and it still failed. Is it a problem of the server?

The 3dna.rutgers.edu server is hosted by Rutgers University. You may get any information on it from Dr. Wilma Olson. I have nothing more to offer on this matter.

You may try DSSR with the --nmr and --json options for MD analysis. As noted recently in the announcement post "DSSR 2.0 is licensed by Columbia University", "DSSR 2.0 supersedes 3DNA 2.4, which is still maintained but no additional features other than bug fixes are scheduled."

Best regards,

Xiang-Jun

13
Hi Mohit,

What "current version of SNAP" did you refer to? Have you tried "x3dna-snap --help"? Please post back the output of running this SNAP command option.

Best regards,

Xiang-Jun

14
Recently, while visiting the NAR website on DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL, I noticed a big red circle near “View Metrics”. The symbol is very obvious and a bit 'alarming'. I was curious to see what it meant. After a few clicks, I was delighted to read the following recommendation in Faculty Opinions by Quentin Vicens:

Quote
I really enjoyed “playing” with the revised and expanded version of Dissecting the Spatial Structure of RNA (DSSR) described by Xiang-Jun Lu in this July issue of NAR. The software is known to generate ‘block view’ representations of nucleic acids that make many parameters more immediately visible, such as base composition, stacking, and groove depth. This new version includes Watson-Crick pairs shown as single rectangles, and G quadruplexes as large squares, making such regions more quickly distinguishable from other regions within an overall tertiary structure. I was amazed at how simple and effective the web interface was, and I liked the possibility to download a PyMOL session to look at molecules under different angles. If need be, blocks can be further edited in PyMOL using the provided plugin (see on page 35). I highly recommend it!

The DSSR-PyMOL schematics paper/website has been rated “Very Good”, and classified as “Good for Teaching”. See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327. A screenshot is attached below.


15
Site announcements / DSSR 2.0 is licensed by Columbia University
« on: August 24, 2020, 08:35:04 am »
DSSR 2.0 is out. It integrates an unprecedented set of features into one computational tool, including analysis/annotation, schematic visualization, and model building of 3D nucleic acid structures. DSSR 2.0 supersedes 3DNA 2.4, which is still maintained but no additional features other than bug fixes are scheduled. See the DSSR 2.0 overview PDF.

DSSR delivers a great user experience by solving problems and saving time. Considering its usability, interoperability, features, and support, DSSR easily stands out among 'competitors'. It exemplifies a 'solid software product'. I strive to make DSSR a pragmatic tool that the structural bioinformatics community can count on.

DSSR 2.0 is licensed by Columbia University. The software remains free for academic users, with the basic user manual. The professional user manual (over 230 pages, including 7 appendices) is available for paid academic users or commercial users only. Licensing revenue helps ensure the long-term sustainability of the DSSR project.

Additionally, the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" has recently been published in Nucleic Acids Research, 48(13):e74. Check the web interface.

The DSSR-PyMOL paper/website has been rated "very good" and classified as "Good for Teaching". See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327.

16
Hi Zikri,

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

Regarding DPA and DSP, you are correct in saying that 3DNA is not able to model them. From the PDB files you attached, 3DNA (reasonably) does not take DPA and DSP as nucleotides at all. Other tools may help. If you find any, please share with us.

Thanks,

Xiang-Jun

17
General discussions (Q&As) / MOVED: RNA Journal Covers
« on: July 28, 2020, 03:38:07 pm »

18
RNA structures (DSSR) / Re: RNA Journal Covers
« on: July 28, 2020, 03:37:38 pm »
Hi Cathy,

Thanks for producing all these RNA Journal cover images using 3DNA/blocview and PyMOL; they look nice. In addition to the post on 2019 covers, I also have an update post for 2020, see http://x3dna.org/highlights/cover-images-of-the-rna-journal-in-2020 and the image below. This post is already a bit dated since it does not include the cover of the August 2020 issue.


I am so glad to know that you have found the DSSR-PyMOL approach much easier to use, and producing better schematics. In addition to the --cartoon-block option you mentioned, users may also want to try the --blocview option. It is the option used for pre-calculated results of PDB entries in http://skmatic.x3dna.org.

For viewers of this thread, I'd say that the supplemental PDF is well worth reading. In concluding the DSSR-PyMOL paper, I wrote specifically:

Quote
Finally, all results reported here are completely reproduceable (see the supplemental PDF). Any questions related to this work are welcome and will be openly addressed on the 3DNA Forum (http://forum.x3dna.org).

Best regards,

Xiang-Jun

19
General discussions (Q&As) / Re: Local base step parameters
« on: July 13, 2020, 02:58:12 pm »
Hi Nicolas,

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

Since 3DNA v2.4 is open source, the best way to dig into the details you are interested is to read the code. The definition of base-pair step parameters is based on SCHNAaP/SCHNArP (), for which the source code is also available.

Depending on the 3DNA version you downloaded, you may find a PDF tech-details.pdf (attached) that provided step-by-step details on how 3DNA base-pair parameters are calculated.

HTH,

Xiang-Jun



20
Hi,

Thanks for your involvement on the 3DNA Forum.

I understand your question conceptually. In the current implementation of the "Composite" module of web 3DNA 2.0, however, there is no "straightforward way" to control the orientation of reference DNA-protein complexes. In principle, this feature should not be hard to implement, given the infrastructure already in place.

The "Composite" module was initially implemented by Guohui Zheng in "Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures" in 2009, and then polished by Shuxiang Li in "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" in 2019. The initial w3DNA website hosted at Rutgers (http://w3dna.rutgers.edu) is no longer functioning. The w3DNA 2.0 website (http://web.x3dna.org) is hosted at Columbia to which I am direct access.

Shuxiang no longer works on the 3DNA project, even though he may still be available for quick answers. However, implementations of new features like this one are not expected from him. Within my capability, I will try to ensure that the web 3DNA 2.0 server works as described in the 2019 publication in Nucleic Acids Research.

Best regards,

Xiang-Jun


PS. Given the many recent and previous questions like yours, I am planning to distill and streamline related modeling utilities in 3DNA v2.4 into DSSR. The w3DNA 2.0 and wDSSR may not be updated in sync, but the DSSR command-line interface will be far more sophisticated. In due course, I may create a new simplified web interface (like http://skmatic.x3dna.org) specifically for the modeling capabilities in DSSR 2.0. 

21
Hi Salvador h.v,

Quote
a) the webserver: http://wdssr.x3dna.org/analyze/. However, I am confused, the obtained results are for the 50 frames or only for the first one? I mean, the results are a statistical average?

The http://wdssr.x3dna.org website was developed by Dr. Shuxiang Li, a former postdoc from the Olson lab at Rutgers. Shuxiang has left a while ago for another position. He may chime in to answer your questions, but I am not sure.

Quote
b) dssr in the terminal using: x3dna-dssr -i=nuclei_50Frames.pdb --nmr
However I got the following message: no models found: ignoring the --nmr option.
...

Please attach your nuclei_50Frames.pdb file together with the specific commands and messages. Reproducibility is the KEY.

Quote
To be sincere, is the first time that I perform MDs of DNA-B. I am just trying to figure out what physical quantities are more suited to quantify the deformation of the DNA.

In this case, you may want to first become familiar with well-documented cases in whatever packages you are using. I am not a practitioner of MD simulations, and I cannot provide advices in that filed. If you want to pursue DSSR further, I'd be happy to guide you through any technical aspects.

Xiang-Jun


22
Hi S h.v,

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

Quote
Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.

Yes, try DSSR with options --md (alias --nmr) and --json.

Quote
Also, I would like to ask, if I have a complete trajectory in some binary format and I convert such trajectory to a pdb file, DSSR would be able to analyze the trajectory? The web version of DSSR seems to handle trajectories for around 50 frames...

DSSR starts from standard PDB or mmCIF format, not any non-standard binary format.

Which web version of DSSR are you referring to? Please be specific.

Xiang-Jun

23
Hi Zhonghe,

Thanks for your follow-up. Yes, the Richardson publications you listed are highly relevant. Did you know that DSSR also calculate suiteness? Using 1msy as an example:

Code: Text
  1. x3dna-dssr -i=1msy.pdb
  2. more dssr-torsions.txt
  3. # A2654 and G2655 are in C2'-endo conformation

Using DSSR, it would be straightforward to survey RNA structures (of your choice) and find all nucleotides with C2'-endo sugars. The results could be easily parsed with the --json option. Moreover, DSSR provides context information.

Best regards,

Xiang-Jun

24
Hi Zhonghe,

The following paper may be of (some) interest to you: Sokoloski, Joshua E., et al. "Prevalence of syn nucleobases in the active sites of functional RNAs." RNA 17.10 (2011): 1775-1787.

Other relevant papers? Please chime in.

Best regards,

Xiang-Jun

25
w3DNA -- web interface to 3DNA / Re: Composite
« on: June 24, 2020, 06:23:49 pm »
Thanks for posting your question on the 3DNA Forum.

My understanding is that the templates for the Composite module (on the Web 3DNA 2.0 website) must be from PDB entries. Shuxiang may chime in with more details.

Best regards,

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.