Setting up 3D-DART with X3DNA

[mlowe]

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:
BASEPARS FIBER    bin

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?

[xiangjun]

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,

Xiang-Jun

[mlowe]

I have successfully been able to run a standalone version of 3D-DART and example files. However, the instructions for using 3D-DART for custom structures cannot be found. Can 3DNA bend the DNA at places and angles that I designate? Do you have instructions? If 3DNA cannot bend the DNA, are you aware of software packages that can?

[xiangjun]

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.