Messages

126

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« on: December 07, 2020, 12:33:28 pm »

The base/amino-acid pairs identified by SNAP are named pseudo pairs (see doi: 10.1093/nar/gkr452). I have never heard of the term "pi-pair" as used in the your initial message. So I was confused as to what it really means.

Using 1oct as an example, a graphical illustration of the A-gln pseudo-pair (A.DA204 and C.GLN44) is attached. It should be clear that it is indeed like a base pair (H-bonds, coplanar).

Please generate a similar graph of a base/amino-acid stacking interaction and post it back. This way you would better understand the differences between the DSSR output sections on pair vs stack. It also helps other viewers of the thread.

Best regards,

Xiang-Jun

127

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« on: December 07, 2020, 08:01:08 am »

Hi Takayuki Kimura,

Please clarify your question by providing concrete examples of "pi-stack and pi-pair" in relation to SNAP output.

Thanks,

Xiang-Jun

128

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« on: November 19, 2020, 01:57:12 pm »

SNAP can be downloaded from the "Downloads/3DNA download" Section of the 3DNA Forum.

Xiang-Jun

129

RNA structures (DSSR) / Re: 3DNA/DSSR download issue

« on: November 18, 2020, 11:19:09 am »

Hi,

You should be able to see the "Downloads" section now.

As of v2.0, DSSR is licensed by Columbia University, and it is only available from the Columbia Technology Ventures (CTV) website.

Best regards,

Xiang-Jun

130

FAQs / Re: license missing in x3dna-v2.4 file (window version)

« on: November 11, 2020, 03:13:00 pm »

Hi Jianhui,

Thanks for your enquiry about 'missing' the 3DNA-v2.4 license file. There is a long and complicated history regarding the 3DNA software and its licensing. Basically, the 3DNA-v2.4 software package is free for academic use, even though no license file is explicitly distributed with the  tarball.

DSSR 2.0, which has completely replaced 3DNA v2.x, has been formally licensed by Columbia University. See the overview PDF: http://docs.x3dna.org/dssr2-overview.pdf.

3DNA 2.x is no longer supported for 'free' as it used to be for the past decade. A paid DSSR license from Columbia is required for future technical support.

Best regards,

Xiang-Jun

131

MD simulations / Re: Superimpose representative cluster of a RNA strand after simulation

« on: November 10, 2020, 06:55:08 pm »

Hi,

Please provide concrete examples to illustrate unambiguously what you what to achieve.

Best regards,

Xiang-Jun

PS. DSSR 2.x (paid version) contains built-in support for the analysis of MD simulations, and advanced features for DNA/RNA modeling. It can also be used to perform sequence-independent search/fitting employing base as well as backbone structures.

132

RNA structures (DSSR) / Re: wDSSR showing invalid ID on a valid PDB ID

« on: November 07, 2020, 09:31:40 am »

Sorry -- wDSSR is no longer supported, as least for now.

If users find 3DNA/DSSR useful and continued support for the project indispensable, you are welcome to make your case/thought publicly in the Forum or sending me email.

See also my response to http://forum.x3dna.org/general-discussions/circular-dna-parameters/.

Xiang-Jun

133

RNA structures (DSSR) / Re: Circular DNA parameters

« on: October 30, 2020, 03:46:34 pm »

Dear Thor,

Thanks for your insightful questions on building perfectly circular DNAs of various sizes. DNA/RNA modeling is a topic of great significance and there is clearly a lack of practical software tools. I'm interested in developing new modeling features in DSSR, a replacement of the classic 3DNA suite of programs. Nevertheless ...

Thank you for developing (and maintaining) this collection of beautiful and practical DNA geometry software!

I've enjoyed maintaining 3DNA for nearly two decades. With NIH funding support over the past 9 years, I created DSSR as a replacement of 3DNA v2.x. Alas, I am now out of luck to continuously serve the community for free via NIH funding support, as it used to be.

DSSR is now licensed by Columbia University. Please buy a license if users find 3DNA/DSSR useful and my service valuable. Think in terms of the time/efforts you would otherwise have to spend. Further support and development of DSSR (including customized applications) will be devoted to paid users only -- that's the new normal.

Best regards,

Xiang-Jun

134

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

135

General discussions (Q&As) / Re: changing some of the RNA sequence of an chain to DNA

« on: September 28, 2020, 11:10:37 am »

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

136

General discussions (Q&As) / Re: changing some of the RNA sequence of an chain to DNA

« on: September 27, 2020, 05:18:15 pm »

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

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

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

137

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).

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

138

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

139

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

140

MD simulations / Re: Unnatural base pair helical parameters

« on: September 10, 2020, 08:18:18 am »

Hi Shaikh,

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

141

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.

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

142

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 07, 2020, 10:21:51 am »

Hi Zhengyue,

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.

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.

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?

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:

• Building a bridge between Curves+ and 3DNA
• Analyzing DNA/RNA structures with Curves+ and 3DNA
• Curves+ vs 3DNA

Best regards,

Xiang-Jun

143

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

144

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 04, 2020, 10:43:54 am »

Hi Moi,

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.

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

145

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 02, 2020, 12:15:15 pm »

Hi Moi,

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.

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

146

DNA/RNA-protein interactions (SNAP) / Re: H-bonding between RNA bases and protein amino acids

« on: September 02, 2020, 12:04:13 pm »

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

147

Site announcements / DSSR-PyMOL schematics recommended in Faculty Opinions

« on: August 31, 2020, 11:31:48 am »

Recently, while visiting the NAR website on DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL, I noticed a big red circle ① 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:

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.

148

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.

149

General discussions (Q&As) / Re: Is it possible to implement an unnatural nucleotide?

« on: August 01, 2020, 11:48:26 am »

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

150

General discussions (Q&As) / MOVED: RNA Journal Covers

« on: July 28, 2020, 03:38:07 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=928.0