WebMol

Java-based protein structure viewer and analysis program

Launch WebMol (Windows: double click on jar file, Linux: java -jar webmol.jar) Load structure in PDB-file format, either by invoking "Open" or, under Linux, as a parameter: java -jar webmol.jar

Example: java -jar webmol.jar https://files.rcsb.org/view/4HHB.pdb

For help/instructions, see "Help"

Reference: Walther, D (1997) WebMol--a Java-based PDB viewer. Trends in biochemical sciences 22 (7), 274-275

Source code available upon request. WebMol was developed at the EMBL (Heidelberg, Germany) and UCSF (San Francisoco, USA) in the years 1996-1999

Author: Dirk Walther walther@mpimp-golm.mpg.de

Unique features, highlights

Analysis of packing geometries of secondary structural elements (axes, distances, and angles)
surface and cavity computations, including surface and volume area computation
interactive distance matrix and Ramachandran plots, with differential Ramachandran map as reference (see https://pubmed.ncbi.nlm.nih.gov/10089363/)
API available (see below)

WebMol API

Class webmol

java.lang.Object
   |
   +----java.awt.Component
           |
           +----java.awt.Container
                   |
                   +----java.awt.Window
                           |
                           +----java.awt.Frame
                                   |
                                   +----webmol

public class webmol
extends Frame

WebMol - Java PDB structure viewing and analysis program Author: Dirk Walther (walther@mpimp-golm.mpg.de) Version March 10, 1998

European Molecular Biology Laboratory (EMBL) June 1996-March 1997 University of California, San Francisco (UCSF) April 1997-1999

Reference: Walther D. (1997) WebMol - a Java based PDB viewer. Trends Biochem Sci, 22: 274-275

Example ("webmolExample.java")

import webmol;

public class webmolExample
{
  
public static void main(String args[])
  {
    int num,add=1,col;
    
    webmol wm=new webmol("pdb1ppt.ent",700,600);
    // webmol wm=new webmol("http://www.embl-heidelberg.de/~walther/JAVA/pdb/1ppt.brk",700,600);
    // reads it across the web
    // webmol wm=new webmol("https://files.rcsb.org/view/1PPT.pdb",700,600);
    // reads it from PDB directly

    num=wm.getNumberOfResidues(); 
    int res=0;
    
    for(int j=0;j<2*num;j++)
    {     
      if(wm.getResidueType(res)=='P') // if amino acid = proline then color yellow
        col=wm.yellow;
      else
        col=wm.current; // current color set by WebMol
      
      wm.select(res,
                wm.SIDECHAIN_VS_SIDECHAIN,
                col,
                wm.THICK);
      
      wm.redraw(500);
      
      if(res==num-1) add=-1;
      if(res==0) add=1;

      wm.unselect(res);
      res+=add;
    }
    wm.close(true);
  }
}

Variable Index

Color to apply for selection highlighting
current: Color to apply for selection highlighting
cyan: Color to apply for selection highlighting
gray: Color to apply for selection highlighting
lilac: Color to apply for selection highlighting
orange: Color to apply for selection highlighting
pink: Color to apply for selection highlighting
red: Color to apply for selection highlighting
yellow: Color to apply for selection highlighting
SELECTED_ONLY: Select method
SIDECHAIN_VS_BACKBONE: Select method
SIDECHAIN_VS_SIDECHAIN: Select method
THICK: thick lines
THIN: thin lines

Constructor Index

webmol(String): launching WebMol with default width and height, upon closing the WebMol frame all Java programs will be exited.
webmol(String, boolean)
webmol(String, boolean, int, int)
webmol(String, int, int)

Method Index

close(): close WebMol
close(boolean): close Webmol and exit (exit=true)/ not exit (exit=false) all current Java programs under which WebMol was running
getChainID(int): returns the chain identifier of residue res
getNumberOfResidues(): returns the number of amino acid residues in the current protein structure
getPDBSeqNum(int): returns the PDB sequence number of residue res as it may differ from the consecutive enumeration used by WebMol
getResidueType(int): returns the amino acid type (one-letter code) of residue res
redraw(): redraw the structure in the WebMol main window
redraw(int): redraw the structure in the WebMol main window
select(int, int, int, int): select a single residue, enumeration of residues is in consecutive order; i.e.
unselect(int): unselect residue
unselectAll(): undo all selections

Variables

THICK

 public static final int THICK

thick lines

THIN

 public static final int THIN

thin lines

current

 public static final int current