Standalone version of 3D-DART (originally developed by Marc van Dijk) for Python 2.x series.
- We recommend to use a virtual environment to install 3D-DART:
virtualenv --python=python2.7 dart
cd dart
source bin/activate
- Install numpy library for Python 2.x:
pip install numpy
- Clone this repository:
git clone https://github.com/haddocking/3D-DART.git- Create X3DNA software folder structure:
cd 3D-DART/software
mkdir X3DNA-linux X3DNA-mac- Download from http://x3dna.org/ your specific architecture version and place it
X3DNA-linuxif GNU/Linux orX3DNA-macif macOS. For example,X3DNA-macfolder should contain:
[3D-DART/software/X3DNA-mac]$ ls
BASEPARS FIBER bin
and more in deep:
BASEPARS/:
ATOMIC Atomic_G.pdb Atomic_U.pdb Block_BP.alc Pxyz.dat RNA_BASES col_mname.dat misc_3dna.par ps_image.par trans_pep.alc
Atomic_A.pdb Atomic_P.pdb Atomic_i.pdb Block_R.alc PxyzH.dat baselist.dat fig_image.par my_header.r3d raster3d.par trans_pep.pdb
Atomic_C.pdb Atomic_T.pdb BLOCK Block_Y.alc README col_chain.dat help3dna.dat ndb_raster3d.par rotz90
FIBER/:
Data Str02 Str05 Str08 Str11 Str14 Str17 Str20 Str23 Str26 Str29 Str32 Str35 Str38 Str41 Str44 Str47 Str50 Str53
README Str03 Str06 Str09 Str12 Str15 Str18 Str21 Str24 Str27 Str30 Str33 Str36 Str39 Str42 Str45 Str48 Str51 Str54
Str01 Str04 Str07 Str10 Str13 Str16 Str19 Str22 Str25 Str28 Str31 Str34 Str37 Str40 Str43 Str46 Str49 Str52 Str55
bin/:
EnergyPDNA.exe anyhelix cehs dcmnfile fiber get_part nmr_ensemble pdb2img regular_dna std_base
alc2img block_atom comb_str del_ms find_pair manalyze nmr_strs r3d_atom rotate_mol step_hel
analyze blocview cp_std ex_str frame_mol mstack2img o1p_o2p rebuild stack2img
- Test running the main script, you should get a similar output to this:
cd /path/to/3D-DART
./RunDART.py--> Performing System Checks:
* Python version is: 2.7.1
* Could not import Numeric package trying NumPy
* Importing NumPy package succesfull
--> Your current working directory is: /path/to/3D-DART
--------------------------------------------------------------------------------------------------------------
Welcome to 3D-DART version 1.2 Thu Apr 2 12:03:14 2020
--------------------------------------------------------------------------------------------------------------
--> Parsing command-line arguments:
Wrong command line
If you see the message above, then 3D-DART is ready.
cd /path/to/3D-DART
./RunDART.py -w NAensemblebuild -f example/struct_*.pdbA brief description of the directories:
| Folder | Description |
|---|---|
| jobnr1-FileSelector | Contains the files you used as input. |
| jobnr2-BuildNucleicAcids | Generates a canonical starting structure of the DNA with the desired sequence. |
| jobnr3-X3DNAAnalyze | Runs a 3DNA analysis over the structure generated in job 2 to obtain initial starting parameters for modeling. |
| jobnr4-ModelNucleicAcids | The actual modeling step. Models are represented as base-pair(step) parameter files. |
| jobnr5-BuildNucleicAcids | Converts the parameter files from job 4 into PDB structure files. |
| jobnr6-X3DNAanalyze | Runs a 3DNA analysis over the modeled structures. |
| jobnr7-NABendAnalyze | Runs a global bend analysis over the modeled structures. |
| jobnr8-PDBeditor | Makes some last-minute changes to the PDB files. This directory contains the final structures. |
In the main directory you will find the log file of your job named 'dart.out' In case you encounter unexpected errors please look into the log file.
If you use 3D-DART please cite:
M. van Dijk and A.M.J.J. Bonvin (2009) "3D-DART: a DNA structure modelling server", Nucl. Acids Res. 37 (Web Server Issue):W235-W239, doi:10.1093/nar/gkp287