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Messages - xiangjun

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1
Site announcements / BioExcel webinar on DSSR
« on: November 23, 2021, 11:38:53 am »
On December 9, 2021, at 15:00 CET, I will present a BioExcel webinar titled "X3DNA-DSSR, a resource for structural bioinformatics of nucleic acids."

For the record, the screenshot of the announcement is shown below:


2
Site announcements / No more grant funding for 3DNA/DSSR
« on: October 30, 2021, 09:58:15 pm »
Due to a lack of governmental funding support, we are no longer able to provide DSSR free of charge to the community. Instead, we offer DSSR Pro for academic purposes for a one-time fee of $1000, which includes one year of developer support as set forth in the license agreement, and can be requested from techtransfer@columbia.edu. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu. DSSR Pro excels in structural bioinformatics of RNA, DNA, and their protein complexes. The software has completely superseded 3DNA, and is being continuously improved. Revenue from licensing supports the development and availability of DSSR.

My focus will now shift to DSSR Pro, and I'm committed to making it a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR Pro would save users a substantial amount of time and effort when compared to competing options. On the other hand, 3DNA and DSSR Basic are obsolete and will no longer be maintained or supported.

I aim to keep the 3DNA Forum up and running so that users may help one another and the material remains available. I may chime in occasionally, but I won't be able to continue serving the community for free as I have over the past decade.


3
As mentioned in my previous response, DSSR Pro has options to handle such cases, among other features.

DSSR Pro's default output reports 146 nucleotides, along with a diagnostic note for the two deformed bases. Such deformed bases can participate in a variety of loops but not in pairing interactions.

Quote
Processing file '6nd42.pdb'
  2.G.248 0.808 -- distorted, without fitted base frame
  2.G.323 0.319 -- distorted, without fitted base frame
    total number of nucleotides: 146

DSSR Pro also has an option that treats those distorted bases as normal for base-pairing interactions.

4
DSSR is behaving as designed. Please see the section "Identification of nucleotides" of  the 2015 DSSR paper:

Quote
A nucleotide is identified if a residue contains at least three base ring atoms and the root-mean-square deviation (rmsd) of the fit falls below a user-definable cutoff. Since base rings are rigid, the rmsd is normally <0.1 Å. To account for experimental error and special non-planar cases, such as 5,6-dihydrouridine (H2U) in yeast tRNAPhe (Figure 2), the default rmsd cutoff is set to 0.28 Å.

The default DSSR cutoff values are based on extensive tests in real-world applications. Any unidentified nucleotide is almost always due to heavy distortions in its base geometry that is 'beyond recognition'. For example, G248 in your attached 6nd42.pdb file has the PyMOL rendered image as attached. Note the N1-C2 distance is 2.2 Å, far larger than ~1.5 Å (the normal covalent C-N bond length).

DSSR Pro has provisions to handle extreme cases like yours.

5
RNA structures (DSSR) / Re: DSSR output
« on: October 07, 2021, 09:47:56 am »
Which version of DSSR are you using?

6
Hi Ying,

Given the information you provided, I can only conclude that there must be some oddity in your structure at the places where 3DNA is unable to detect the base pairs. I cannot provide any further advice before seeing the structure (or the relevant section of it).

Xiang-Jun

7
Please provide a concrete example.

8
RNA structures (DSSR) / Re: How to get DSSR up and running?
« on: September 15, 2021, 11:56:26 am »
Hi Ying,

Quote
I am sorry that I forgot to update you on the progress.
Yes. I have downloaded the DSSR basic.


It is beneficial to update each topic you began so that other readers have a complete knowledge of what has occurred.

Quote
After I downloaded the DSSR software, I decompressed it and there are two files (DSSR manual and x3dna-dssr.exec) without further installation. I tried both computers, attached please find two images after I opened the .exec file. It seems that the software did not work. Is there anything wrong?

DSSR was designed with simplicity in mind. There are just two files distributed: a self-contained binary executable [x3dna-dssr (macOS and Linux) or x3dna-dssr.exe for Windows] as well as the associated PDF user manual. Because DSSR is a command-line software, it must be executed from a terminal window.

From the screenshot you attached, you are on macOS and DSSR is running as expected. Presumably, you've double-click x3dna-dssr to run it, as shown below:
x3dna-dssr ; exit;

So DSSR simply prints some help message and then exit. You must have a basic understanding of how to execute command line programs on macOS to run DSSR.

missing required option: must specify -i=PDBFile/mmCIF

type: 'x3dna-dssr -h (or --help)' for further help
      'x3dna-dssr --citation' for preferred citation(s)

Time used: 00:00:00:00

[Process completed]



Quote
Next, let me explain why I want to download the software DSSR. I used the 3DNA web sever before, but there are several base pairs missing, which may result in the incorrect calculation for the width of the major and minor groove of our RNA structure. I searched the forum and found that it may be due to the default setting for the website.  So I want to download the software and reset the parameters to see whether it can recognize the base pairs and measure the width again.

3DNA v2.4 is open source and is available to academic users after registering on the 3DNA Forum. If you have any particular queries about 3DNA v2.x, please submit them in the "General discussions (Q&As)" or "w3DNA — web interface to 3DNA" section.

Quote
In addition, I tried the DSSR web server, it failed because there was an error: Data too long for column 'jobid' at row 1. I also tried to analyze one published RNA structure (4j50)

Web DSSR (http://wdssr.x3dna.org) is an unpublished work, therefore bugs are to be expected. However, it generally behaves as designed. I've just tried PDB entry 4j50 without a problem.

Please remember to include specifics so that others can REPRODUCE reported problems.

Quote
I found that there is no information about the groove width of the helix from DSSR web. So I wonder if the information will be provided by DSSR basic version?

DSSR Basic does not include some features of 3DNA v2.4; DSSR Pro does. As noted on the post "Clarification on DSSR licensing",  "DSSR Basic includes features described in the three DSSR papers (2015 DSSR, 2017 DSSR-Jmol, and 2020 DSSR-PyMOL, all published in NAR) so that reported results can be reproduced."



Users are encouraged to post any 3DNA/DSSR-related queries on the Forum. Please keep in mind to be detailed and to offer follow-up on each thread.

Best regards,

Xiang-Jun

9
RNA structures (DSSR) / Re: Where to download the DSSR basic version
« on: September 13, 2021, 10:16:10 am »
Hi Ying,

Thanks for your follow up. DSSR-related issues are always welcome.

I can see your registration for a DSSR Basic license, as given by the CTV, as of this writing. It is now Monday morning (New York time), which may explain the delay you are experiencing. DSSR licenses are often processed quickly by the CTV support staff. Please keep us informed on your progress. If you haven't heard back from CTV by the end of the day, I'll contact them about your situation.

Best regards,

Xiang-Jun

10
RNA structures (DSSR) / Re: Where to download the DSSR basic version
« on: September 10, 2021, 11:18:59 pm »
Hi Ying,

DSSR may only be downloaded from the Columbia Technology Venture (CTV) website. I've included a link to the CTV website in several places on this 3DNA Forum. I'm surprised that users like you are still having trouble locating where to get DSSR.

To clarify, I changed the header link "DSSR License" to "DSSR Download/Licensing". The DSSR download link is also included in my signature at the bottom of each of my posts. See also the post "Clarification on DSSR licensing".

Registration on the 3DNA Forum is required in order to obtain the classic 3DNA v2.4 (and SCHNAaP/SCHNArP), and ask 3DNA/DSSR-related questions.

Please let me know if there is anything else I can do to make this message crystal clear.

Best regards,

Xiang-Jun

11
As a followup, DSSR Pro now has the option to derive only pairs across chains.

12
DSSR Basic does not have the base mutations feature at all. Also note that DSSR Basic is provided AS IS without any warranty of support.

That said, DSSR Basic does include features described in the three DSSR papers (2015 DSSR, 2017 DSSR-Jmol, and 2020 DSSR-PyMOL, all published in NAR) so that reported results can be reproduced. The DSSR Basic manual should function as expected. Anything to the contrary will be considered a bug and will be fixed as soon as possible.

DSSR Pro includes new advanced features, plus all functionality of 3DNA v2.4, as well as full support. Please watch the DSSR Overview Video.

Instead of DSSR/3DNA v2.4, you may want to try other software tools such as RNAView, FR3D, MC-Annotate, or Curves+ etc. Please let us know what you find.

Best regards,

Xiang-Jun

13
Quote
Through another attempt, I found a solution to the problem.

Please elaborate on what you did that resulted in a solution to the problem.

Thanks,

Xiang-Jun

14
General discussions (Q&As) / Re: 3DNA manual
« on: July 28, 2021, 09:16:09 am »
Check the $X3DNA/doc folder.


Remember to post specific questions in a new thread with a clear subject line.

Reading posts linked at "Netiquette" at the upper-left corner of the Forum should help.

Best regards,

Xiang-Jun

15
Hi chen long,

Quote
1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.

This is the first time I've heard of problems installing DSSR on Windows and Linux.

I do not understand what you mean by "But the windows version of the exe installation package can't open all the time." Does it work sometime? If so, when and under what condition? What do you mean by "it doesn't work"? Please provide screenshots to illustrate unambiguously the issues you experienced.

Quote
2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time.

Then what format do you have from CTV download set? How long have you tried to find any other installation format?

It is fashionable these days to discuss the reproducibility of scientific publications. It's also crucial to ask questions in a consistent manner.

Best regards,

Xiang-Jun

16
DSSR Pro can do it and more.

Xiang-Jun

17
RNA structures (DSSR) / Re: how to repair a DNA model
« on: July 27, 2021, 11:48:48 am »
Please provide some background info and a concrete example to illustrate unambiguously what you want to achieve.

Thanks,

Xiang-Jun

18
Quote
Yes, I tried and finally manage to color differently at each nucleotide blocks.

Glad to know that you have managed to color nucleotide blocks as desired. This is an important first step for later on speed optimizations.

Quote
But it is quite slow since it make all individual block object for every nucleotide.


How many colors do you want to have? Grouping nucleotides with the same color should speed up the process. It is now a matter of PyMOL selection syntax to play with.

Quote
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

I cannot reproduce the warning messages. Let's not worry about them right now.

Best regards,

Xiang-Jun


19
Bug reports / Re: Uncaught exception error
« on: July 21, 2021, 09:50:10 pm »
Hi,

The DSSR version you used is v1.9.4-2019jul08. The latest DSSR version is v2.3.2-2021jun29, which works as expected for PDB entry 6jwe, as shown below:

Code: [Select]
x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json

Processing file '6jwe.pdb'
    total number of nucleotides: 20
    total number of base pairs: 18
    total number of helices: 2
    total number of multiplets: 4
    total number of atom-base capping interactions: 2
    total number of splayed-apart dinucleotides: 2
    total number of non-loop single-stranded segments: 1
    total number of G-tetrads: 3
    total number of G4-helices: 1
    total number of G4-stems: 1

So please update your DSSR to the latest version (available exclusively from Columbia Technology Ventures).

Best regards,

Xiang-Jun



20
RNA structures (DSSR) / Re: Classical RNA loop motifs
« on: July 19, 2021, 08:49:19 am »
Hi Dr. Baulin,

Quote
As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

You may be right. Your list of 'classical RNA loop motifs' includes `etc.` and I am not sure/aware of the complete list.

Quote
As I know it:
1) only kink-turns are annotated by DSSR.

DSSR isn't intended to be a comprehensive tool for annotating 'classical RNA loop motifs.' DSSR, on the other hand, includes the fundamentals (such as base-pairing/stacking annotations and backbone torsions) that should make any downstream pipeline easier to annotate any well-defined RNA structural motifs.

DSSR can auto-detect kink-turns because K-turns have striking structural features and important functional roles, and I want to have a thorough understanding of the motif. Personally, I've found that only by implementing a topic/concept in detail source code can I truly comprehend it.

The Tamar Schlick made use of this DSSR features in their 2017 NAR paper "Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction." Please take a look at the following two threads (which also demonstrate the value of the 3DNA Forum) initiated by lead author of the paper:

Quote
2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.

RNAMotifContrast and RNA Motif Atlas clusters are certainly well-known resources on the topic. Another source of information that is worth checking is the Janusz Bujnicki lab website.

Quote
3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

DSSR has a dedicated section of ALL internal loops. Filtered by sequence constraints and geometric constraints, you might find what you're looking for.

Quote
If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

In the future, I may add more motif annotations to DSSR Pro.

Best regards,

Xiang-Jun

21
In principle, I understand what you're trying to accomplish. However, I am unable to provide any concrete answers due to a lack of information.

22
Please pay close attention to my requests for clarification.

23
Code: [Select]
X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;

Are you sure this is the dot-bracket notation, with desired base-pairs you want???

24
What the .dbn should be in this case (2YIE, between chains X and Z)?

25
Please give specific examples of what you want to accomplish so that others can assist you. It's also a good way to get your thoughts straight.

Pages: [1] 2 3 ... 62

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.