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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
2
Hello,

I am currently using a synthetic DNA that has two unnatural nucleotides, Cu(II)-DPA and dSpacer (DPA and DSP, pdbs attached). In my DNA, these two nucleotides are paired to each other as shown in the following.

5'-AAT ATT AXA GAT ATC TYT TTA TAA-3'
3'-TTA TAA TYT CTA TAG AXA AAT ATT-5'

where X is DPA and Y is DSP.

Is it possible to submit the unnatural Cu(II)-DPA and dSpacer PDB into the 3DNA software for building my synthetic DNA? I understand that one can edit the baselist.dat file to have a modified base in the library. However, i assume that modified bases are possible due to their commonalities with the canonical nucleotides and their ability to form hydrogen bonds for their pairing. Because my nucleotides are not based on the canonical nucleotides, I suspect that 3DNA might not be able to take my unnatural nucleotides' PDB and model my synthetic DNA. However, I would double check if it is impossible for me to model my synthetic DNA.

Regards,
Zikri
3
General discussions (Q&As) / MOVED: RNA Journal Covers
« Last post by xiangjun on July 28, 2020, 03:38:07 pm »
4
RNA structures (DSSR) / Re: RNA Journal Covers
« Last post by xiangjun 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
5
RNA structures (DSSR) / RNA Journal Covers
« Last post by cllawson on July 28, 2020, 02:55:31 pm »
Ha just found this http://docs.x3dna.org/images/3dna-RNA-covers.png
Thank you Xiang-Jun for collating all of the 2019 journal covers I had created using X3DNA/blocview with pymol.
I have been testing out x3dna-dssr --cartoon-block today and it is much easier!
I will be using this great new option for all future NDB requests for covers.  :)
6
General discussions (Q&As) / Re: Local base step parameters
« Last post by xiangjun 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


7
General discussions (Q&As) / Local base step parameters
« Last post by nicalleb on July 13, 2020, 02:23:34 pm »
Hello everyone,

I study the ionization of small complexes composed of several stacked DNA bases. The values of ionization potentials seem to be very dependent of the conformational parameters. I use web-X3DNA to determine the local base step parameters (shift, slide, rise, tilt, roll and twist) of my complexes. I would understand how these parameters are determined by the software (because My results are very variable).

In that purpose, I looked for information in the tutorial and in some articles related to the program but it doesn't really help me. I've namely found that X3DNA adopts the standard reference frame for the parameters but again, it doesn't help me much. Do you have detailed information about the determination of the parameters by X3DNA or can you indicate me where I can found more precise information ?

Thank you in advance,

Nicolas (PhD student at ULB, Belgium)
8
w3DNA -- web interface to 3DNA / Re: Binding site orientation in Composite
« Last post by xiangjun on July 12, 2020, 07:25:14 pm »
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. 
9
w3DNA -- web interface to 3DNA / Binding site orientation in Composite
« Last post by ab9010 on July 12, 2020, 01:33:37 pm »
Is there any straightforward way to invert protein binding site on DNA? Since many DNA-binding protein complexes are not symmetrical, nor their recognition sequence on DNA is symmetrical, I noticed that the tool automatically interprets the 'binding site' from the reference PDB in just one of the two possible orientations. Any clue on how to select the second orientation of the binding site to make the model through Composite?

e.g.  my seq:  aaaaaaATTGGaaaaaaaaaaaGAGATaaaaaaaa  (uperrcase are the two binding sites)

     ref pdbs:        aaaATTGGaaa           aaATCTCaaa
                   protein1 (correct orientation)    protein2 (the tool selects the complementary chain as reference, so the protein is also inverted in the final model)

Thank you in advance
10
RNA structures (DSSR) / Re: Analysis of trajectory from Molecular Dynamics
« Last post by xiangjun on July 08, 2020, 02:55:19 pm »
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

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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.