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Messages - xiangjun

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1
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

3
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

4
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



5
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. 

6
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


7
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

8
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

9
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

10
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

11
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« on: June 20, 2020, 12:23:58 pm »
As a follow-up of my previous response, I would like to clarify the following points:

  • The binary executables of DSSR is named x3dna-dssr in macOS and Linux, and x3dna-dssr.exe in Windows, per conventions in the Unix-like and Windows operating systems.
  • After downloading x3dna-dssr in macOS and Linux, users should run chmod +x x3dna-dssr to set the execute permission. The x3dna-dssr file at the download site actually has this execute permission; for security reasons, it is switched off during the downloading process.
  • The binary executable of DSSR is < 2MB. It is completely self-contained. No hundreds of MB even GB of a download to un-package/install; no configurations; no dozens of dependencies. Such complicated things users may get used to nowadays simply do no exist in DSSR.
  • Getting DSSR up and running has never been an issue over the past eight years, even (especially) with beginners. The instruction given here should be sufficient for the majority of users to get started with DSSR. The DSSR User Manual contains detailed installation instructions and common usages. The manual is well worth reading not only for DSSR users but also for those interested in nucleic acid structural bioinformatics.

Best regards,

Xiang-Jun

12
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« on: June 18, 2020, 06:30:47 pm »
Dear Roland,

Thanks for your interest in DSSR. The binary file x3dna-dssr is all it is. Assuming you have downloaded the macOS or Linux version, simply run "chmod +x x3dna-dssr" to make it executable. Then you're all set. By design, the simplicity with DSSR is out of the norm. One may even feel it anticlimactic in the big data, bloated software era.

Check with "x3dna-dssr -h" for further information. See the DSSR User Manual for details (http://docs.x3dna.org/dssr-manual.pdf). If you have any further questions, please do not hesitate to ask.

Best regards,

Xiang-Jun

13
w3DNA -- web interface to 3DNA / Re: Base pair in 3LZ0 not recognised
« on: June 16, 2020, 07:28:00 am »
Hi Maik,

Quote
After installing 3DNA and tweaking the parameter file the missing base-pair is recognised!

Glad to hear that it works. For the benefit of other viewers of this thread, could you please provide details on what you did to solve this specific problem?

Thanks also goes to Shuxiang, who is helping out this Forum from the sidelines.

Best regards,

Xiang-Jun

14
w3DNA -- web interface to 3DNA / Re: Base pair in 3LZ0 not recognised
« on: June 15, 2020, 09:29:20 pm »
Hi Maik,

In addition to what Shuxiang has suggested, have a look of FAQ entry How to fix missing (superfluous) base pairs identified by find_pair?. Specifically, using the 3DNA command-line find_pair/analyze programs should do the trick.

Best regards,

Xiang-Jun

15
General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA
« on: June 06, 2020, 09:54:43 am »
The 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool) provides a convenient means of generating custom 3D structural models of DNA with control over the local and global conformation.

3D-DART uses the DNA rebuild functionality of the well-known software package 3DNA Lu et al. and extends its functionally with tools to change the global conformation of the DNA models.

Please ask the 3D-DART developer for related questions.

As far as 3DNA itself is concerned, please refer to the 2008 Nature Protocol paper and the 2013 JoVE for its rebuilding features with worked examples. See also the "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" paper for related modeling tools.

16
RNA structures (DSSR) / Re: dssr stdin
« on: May 31, 2020, 11:37:20 am »
Quote
If there is source code for dssr, I am happy to help with implementing such a feature.

Regarding the availability of DSSR source code, please see the thread "Source distribution/Linux packaging" (http://forum.x3dna.org/rna-structures/source-distributionlinux-packaging/). DSSR 2.0 (to be released) will be formally licensed by Columbia University.

There are open source alternatives to DSSR, including MC-Annotate, RNAView, and FR3D, that may better suit your needs.

BTW, does the suggested method work? As a general principle, the user who starts a thread is expected to provide a summary, or at least a simple yes/no response. Other viewers of the thread will benefit from your effort. It will also give me more incentive to answer your future DSSR-related questions (if any).

Best regards,

Xiang-Jun

17
RNA structures (DSSR) / Re: dssr stdin
« on: May 30, 2020, 11:56:43 am »
Quote
Can x3dna-dssr uses stdin for input?
Yes.

Quote
The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-

When piping input to DSSR, users must specify the file format via --format. Assuming file.pdb is in PDB format, the following should work:

Code: [Select]
cat file.pdb | x3dna-dssr -i=stdin --format=pdb
cat file.pdb | x3dna-dssr -i=- --format=pdb

Please have a try and report back how it goes.

Best regards,

Xiang-Jun

18
General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA
« on: May 28, 2020, 12:46:39 am »
The attached file "x.out" has the following content:

Quote
handling file <struct_1_fixed.pdb>

Time used: 00:00:00:00
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP1' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP2' atom : residue name 'THY', chain B, number [  27 ]
missing ' P  ' atom : residue name 'THY', chain B, number [   1 ]
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]

This means 3DNA v2.4.4 itself is running properly.

However, the file also contains "EnergyPDNA.exe: command not found". EnergyPDNA.exe is not part of 3DNA, v1.5 or v2.x. It could be part of 3D-DART.

From 3DNA v1.5 to v2.x, there is indeed reorganization of data folders, including:
Code: [Select]
BASEPARS ---> config
Examples ---> examples
FIBER ---> fiber

The most important one is BASEPARS ---> config.

For your convenience, I have dug out 3DNA v1.5, and sent you an email with links for download.

Note that 3DNA v1.5 is no longer supported. Even 3DNA v2.x is under maintenance mode: no more new features, only bug fixes. All new developments are devoted to DSSR and SNAP, which supersede 3DNA.

Best regards,

Xiang-Jun





19
SNAP is an analysis tool. Schematic visualization is beyond its design scope.

Have a look of http://skmatic.x3dna.org. Is there anything useful there?

Xiang-Jun

20
Hi Tom,

Thanks for your interest in implementing the DSSR algorithm for identifying base pairs. You are correct that the two bases in a pair are usually not parallel. Thus the mean the two z-axes is used for calculating the vertical separation (i.e., Rise).

Detailed description of the algorithm can be fond in the paper "Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP)" (https://doi.org/10.1006/jmbi.1997.1346). The exact algorithm in SCHNAaP was then adapted to 3DNA, and DSSR. The source code of SCHNAaP is available.

Best regards,

Xiang-Jun

21
As a follow-up of this thread, DSSR 2.0 (to be released soon) contains a new module for in silico base mutations with great flexibility and convenance. It can mutate all of the A's to G's except for residue 5 and residue 7, for example.

The 'mutate_bases' program is obsoleted. No program named 'x3dna-mutate' will be distributed.

Xiang-Jun

22
General discussions (Q&As) / Re: basepair centers
« on: April 28, 2020, 11:43:21 pm »
Hi Daniel,

Thanks for posting an example to make your point clear.

The numerical values you provided for the origins of the two base-pairs at the termini are correct.

I've heard of the term "end-to-end distance of the entire DNA" many times, but never used it in my own work. I'm just wondering what is the end-to-end distance of a circular DNA. Do you have any idea on that?
Best regards,

Xiang-Jun

23
General discussions (Q&As) / Re: basepair centers
« on: April 28, 2020, 06:27:50 pm »
Hi Daniel,

Quote
I still need to calculate the end-to-end distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna?

Could you please be specific what you mean here, using a concrete example?

Xiang-Jun

24
RNA structures (DSSR) / Re: Identify sugar type in the DSSR output
« on: April 23, 2020, 02:39:19 pm »
I've just updated DSSR to v1.9.10-2020apr23. It has a new field named "nt_type", with possible values of "DNA", "RNA" or "unknown". Since the item is included in the nts[] array, I've used the name "nt_type" instead of your suggested "nt_sugar_type" (with values of "ribose" or "deoxyribose" etc).

Please download the updated DSSR (forget about the label, which still reads "v1.9.9-2020feb06"), and report back how it goes.

Best regards,

Xiang-Jun


Pages: [1] 2 3 ... 58

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.