Programs

This page provides some programs that can be used in biomolecular dynamic calculation.

Structure-selection

usage: ./mc-new.x (experiment file) (calculate file list) (number of MC steps) (number of conformers) (outputfile)

the experiment file contain two column, one of the residue number and one of the sPRE value

the calculate file list just need to specifiy the name of the calculate sPRE file (also contain two column same as the experiment file)

Resource files: 
AttachmentSize
Binary Data mc-new.x941.39 KB

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.

 

Download

The binary file can be freely downloaded here. (upgraded on 18 Nov.)

Install

The program runs on Linux. It depends on X environment and xplor-nihJava 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

sPRE.x

Install : tar xjvf sPRE.tar.bz2; chmod a+x sPRE.x

Usage : ./sPRE.x (pdb file) (Rprobe) (Dpara) (Atom)

Rprobe: the size of paramagnetic probe Dpara : the concentricity of paramagnetic center, 0 means right at the center Atom : the name of atom used for sPRE calculation, which is listed in the third column of the pdb file. 'HM' represents protons of methyl group

Resource files: 
AttachmentSize
Binary Data sPRE.tar.bz2276.35 KB