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1
Site announcements / BioExcel webinar on DSSR
« Last post by xiangjun 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
General discussions (Q&As) / installation error in MAC
« Last post by dnalectronics on November 22, 2021, 02:16:43 pm »
I tried to install x3DNA in mac and it shows "-bash: final_pair:command not found".
I went to bin and clicked on x3dna set up and it showed that I need to copy export X3DNA and PATH to ~./bashrc file. I went to terminal and created a bashrc file and copied the above things. Now I tried to run source ~/.bashrc, I think it was successful but when I typed final_pair -h it shows error. Can you please help me in solving this error?

Thank you!
3
Site announcements / No more grant funding for 3DNA/DSSR
« Last post by xiangjun 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 The software has completely superseded 3DNA, and is being continuously improved.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.

4
MD simulations / Re: generate DNA pdb file for Gromacs
« Last post by dnalectronics on October 27, 2021, 01:00:46 pm »
Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.
5
MD simulations / DNA step parameters
« Last post by dnalectronics on October 27, 2021, 09:18:45 am »
I am an experimentalist working on DNA-drug binding. However, to support my result I am trying to do simulation. Since I don't have an experimentally determined structure for my custom 12-mer DNA duplex, I have to create one from scratch. I am using  w3dna.rutgers.edu,  to create a wide variety of nucleic acid structures.  However, I want to know what is base parameter file or where can I get that file.

I will really appreciate if you can please guide me.

Thank you for your help.
6
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.
7
This is probably misleading. For the sake of calculating base pairs, I completely agree that we should not consider nucleobases with highly distorted conformation. However, when counting how many nucleotides are there in the sequence (e.g., when generating ct or dbn files), nucleotides with distorted base conformation (or even nucleotides without their base groups) are still nucleotides. It may not be a good idea to just delete them from the sequence without at least printing out a warning message.
8
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.
9
RNA structures (DSSR) / dssr did not recognize some canonical nucleotide in 6nd4 chain 2
« Last post by zcx on October 21, 2021, 07:52:52 pm »
I am using dssr version v1.9.10-2020apr23 to analyze PDB 6nd4 chain 2. There are 146 standard nucleotides in this chain. However, when I run

x3dna-dssr -i=6nd42.pdb  -o=output.dssr

It reports
    total number of nucleotides: 144

This also causes the dssr-2ndstrs.dbn files to have 144 rather than 146 positions. It seems dssr disregard residue G248 for unknown reason.
10
RNA structures (DSSR) / Re: DSSR output
« Last post by xiangjun on October 07, 2021, 09:47:56 am »
Which version of DSSR are you using?
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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.