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General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA
« Last post by xiangjun on Today at 12:46:39 am »
The attached file "x.out" has the following content:

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,


General discussions (Q&As) / Setting up 3D-DART with X3DNA
« Last post by mlowe on Today at 12:21:38 am »
On a Mac, I am trying to install 3D-DART, which uses X3DNA. However the installation failed. The output and error messages are shown in the attachment. It's possible that 3D-DART was designed to use X3DNA v. 1.5. Using the current version of X3DNA (3DNA v2.4.4-2019sep09), this is what I see:

The problems seem to develop when 3D-DART tries to run the plugin X3DNAanalyze.

I noticed that my subdirectories are different from the ones listed on the 3D-DART website, which says that I should see:

However after installing 3DNA, I have these directories:
config     fiber    bin

The files in BASEPARS appear to be in config.
The files in FIBER appear to be in fiber.
The files in bin are still in bin.

In addition, based on looking for a similar issue on the web, it is possible that EnergyPDN.exe will not run correctly.
Any suggestions?
DNA/RNA-protein interactions (SNAP) / Re: Visualization of SNAP output
« Last post by xiangjun on May 15, 2020, 12:20:17 pm »
SNAP is an analysis tool. Schematic visualization is beyond its design scope.

Have a look of Is there anything useful there?

DNA/RNA-protein interactions (SNAP) / Visualization of SNAP output
« Last post by Aleix_TS on May 15, 2020, 11:58:05 am »
Hi Xiangju, I have a maybe silly question. I am able to run SNAP  with my protein-DNA structure, I would like to know how could I output a diagram to visualize them on a schematic DNA structure.

RNA structures (DSSR) / Re: Identification of Basepairs - Vertical Seperation
« Last post by xiangjun on May 15, 2020, 10:10:12 am »
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)" ( The exact algorithm in SCHNAaP was then adapted to 3DNA, and DSSR. The source code of SCHNAaP is available.

Best regards,

RNA structures (DSSR) / Identification of Basepairs - Vertical Seperation
« Last post by Tom Mülller on May 15, 2020, 03:47:55 am »
Dear Xiang-Jun,

I am a student at the Technical University Darmstadt, Germany and I am
trying to implement your criteria for the identification of base pairs as described in your 2015 NAR paper.

The second criterion is that the vertical separation between the base
planes is <2.5A. However, as the planes of any two bases are usually not
parallel I am unsure how to calculate the vertical separation.

Could you please clarify the proper algorithm for calculating the
vertical separation between the two base planes?

Kind Regards

Tom Müller
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.

General discussions (Q&As) / Re: basepair centers
« Last post by danielsalgado on April 29, 2020, 10:59:52 am »
Hi Dr. Xiang-Jun,

I'm rather used to modeling cows as discs in a 2d space  :P , so I can't say I'm uncomfortable with this simplification of the DNA, but I see your point.

Thank you for taking the time to help me. Nice tool by the way, it's been incredibly helpful for analyzing the results of my simulations.

Best regards,

General discussions (Q&As) / Re: basepair centers
« Last post by xiangjun 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,

General discussions (Q&As) / Re: basepair centers
« Last post by danielsalgado on April 28, 2020, 11:22:38 pm »
Hi Dr. Xian-Jun,

thank you for your response.

I think I've finally understood how to obtain the information I'm looking for, which is the origin of each basepair. I am attaching one snapshot of the simulations I've performed in pdb (and the result of find_pair). In this case, what I'm interpreting as the end-to-end distance corresponds to the distance between the origin of the A-T base pair at (166.994, 190.835, 4.669) and the G-C basepair at (146.156, 129.39, 144.990), does this make sense? Could this be interpreted as the center of a basepair?

Best regards,

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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.