DynaXL

  • Posted on: 13 July 2016
  • By: liuk

As described in the paper

Modeling protein excited-state structures from "over-length" chemical cross-links

Yue-He Ding, Zhou Gong, Xu Dong, Kan Liu, Zhu Liu, Chao Liu, Si-Min He, Meng-Qiu Dong and Chun Tang, J Biol Chem, 292,1187-1196 (2017)

Contact: tanglab@wipm.ac.cn

What is DynaXL

DynaXL lets you to select a local PDB file of your protein, jot down the residues involved in the cross-link and the type of cross-linker. Here each node stands for residue number, and each edge stands for the corresponding crosslinker. You can draw the cross-links you have identified experimentally in any layout. The calculation script will be generated automatically, which can be invoked in Xplor-NIH.

 

How to use DynaXL

Download

The binary file can be freely downloaded here. (upgraded on 18 Nov 2016.) Source code can be found at github.

Install

The program runs on Linux. It depends on X environment and xplor-nih. Java version above 1.8 is necessary.

tar xjvf DynaXL.tar.bz2 -C ~/ cd ~/DynaXL chmod a+x ./DynaXL.sh

Run

cd ~/DynaXL ./DynaXL.sh

Tips

  • The program was tested on Ubuntu 16.04 and xplor-nih 2.42. On mac os sierra with xplor-nih 2.42 it seems have some bugs, which may be fixed later,
  • Xplor-nih depends on bc, which is installed by default on most linux distributions, but if your distribution (like ArchLinux dose not ship it by default), please install it by the hand.
  • Make sure that the original PSF file before cross linker patching was generated correctly in the step 2. In this step, we provide two optional way to generate the PSF file. You can choose the “semi-automatically generate the PSF” if your PDB file was in standard format without special amino acids or atoms or residues missing, otherwise, I recommend you to prepare the original PSF file preliminary and select the “choose a PSF file”. If you choose the semi-automatically generate the PSF, please check the PDB file carefully according to the PSF file, especially the ending (see figure below). Sometime the xplor will add an extra oxygen atom for the last residue and rename the last two oxygen atoms as OT1 and OT2 in the PSF file, which will make the inconsistent for the PDB file and PSF file. A simple way to deal with this situation is copy the last line of the PDB file and rename the last two oxygen atoms as OT1 and OT2. 
  • After you draw the topology diagram of cross link and define domains, you can click the step 5 to generate script and run the step 6. The PDB and PSF file with cross linker patched will generated at the beginning of the step 6, you can visualize the PDB file to check whether the cross linker were patched correctly. After that, you can leave the DynaXL away and run the xplor independently. 

Changelog

  • 18 Nov. 2016: add features -- users can define the size of EnsembleSimulation.
  • 13 July 2016: the first public version