How to perform a Voronoï tessellation with Voro3D ?

• Select a protein structure file (PDB format .pdb, .ent) : File > Open PDB file 
• The environment option window appears
• In the first frame, enter a name (four characters, for instance 1bhp). This name will be used for all the output files related to the analyzed structure
• Do you want to embed your structure in our environment ? select yes or no. For details see : Angelov et al "Nonatomic solvent-driven Voronoï tessellation of proteins : an open tool to analyse protein folds" Proteins : 2002;49:446-456
• You can select the points reprensenting amino acids :
1. alpha carbons
2. beta carbons (alpha carbon for glycine)
3. geometric centers of all the side chain atoms (hydrogen atoms are not considered)
4. geometric centers of all the side chain atoms and alpha carbons (hydrogen atoms are not considered)
5. geometric centers of all the amino acid atoms (hydrogen atoms are not considered)
• You can choose the environment sphere radius (default value 6.5 angstroms)
• You can choose the number of environment layers around the protein (default value 3.5)
• Do you want the environment (and the structure) coordinate output file ? select yes or no (file name : 1bhp_envir0)
• press validation
• The trace of the protein (white), the representative points (red) and the environment sphere centers (blue) appear in the small 3D window
• The yellow frames indicate the available output files and their location. If you double-click on a file name, the file opens in another window
• To avoid discrepancies at the protein surface you can relax the environment : press relaxation
• The relaxation option window appears
1. Choose the number of relaxations (9 is the default value but 6 are usually enough)
2. For each relaxation you can have the coordinate file : select yes or no (file names : 1bhp_R1 to1bhp_R15)
3. If you only want the last one : select yes or no
4. The relaxations can be stopped if at least one amino acid is not in the bulk (its corresponding cell is an infinite one) : select yes or no
5. Press validation
   
• To perform the tessellation press relaxation
• The tessellation option window appears
1. Do you want to have a weighted tessellation (Laguerre polyhedral decomposition) : select yes or no
2. When you choose yes you can press on the change the weights button
• The weights window appears
• XXX represents the environment
• Increasing an amino acid weight is giving more importance to that particular kind of amino acid (i.e. their cells will be bigger)
• For details see : Sadoc et al "The Laguerre polyhedral decomposition : application to protein folds" Eur, Phys. J. B. : 2003;33:355-363
3. Press validation
• After calculation the protein trace and the superimposed tessellation appears in the main 3D viewer
• The cell table (left hand side) is completed, in this table, each line corresponds to an amino acid. From left to right : 
• The amino acid name (one letter code), the amino acid number, the amino acid chain
• The cell volume, the cell surface (angstrom), the number of faces, the position (V : volume, S : surface,  in this last case the cell is infinite)
• If you click on +, a table appears (the face table). Each line of this new table corresponds to one face of the considered cell. From left to right : 
• numbering of the different contact faces, neighbor name (one letter code), neighbor number (corresponding to the cell table), its chain
• the number of sides, the face area, its perimeter, the distance between the two representative points
  
• The following 6 columns correspond to graphic parameters. For columns cell, trac, all, labl and tra the squares are coloured yellow (position : on) or gray (position : off). To switch from one position to the other, just click on the corresponding square. For the entire column, you may click on its title. A left-click enables every square, a right-click disables them.
• cell : the corresponding cell appears (yellow square) or disappears (gray square). 
• trac : the corresponding trace appears or disappears
• all : all the corresponding atoms appear or disappear
  
• labl : the corresponding label appears or disappears
• col : you can choose the cell color. If you click on a square, a classical color window appears from which you can change color. If  you click on the column title, the cell color window appears. Then, you can select other colors for each kind of amino acid or for all of them (all button). The default colors correspond to hydrophilic/ hydrophobic properties of residues (blue for hydrophilic to red for hydrophobic).
• tra : the cell is transparent or not
•  IMPORTANT : to take these changes into consideration you must press the visualization button
  
• EXP corresponds to the environment accessibility (in %). This is the ratio between surface of faces in contact with environment cells and the entire cell surface.
• If the tessellation is performed on alpha carbons you can press the assignment button to obtain the VoTAP secondary structure assignment. For details see : Dupuis et al "Protein secondary structure assignment through Voronoï tessellation" Proteins :  2004;55:519-528
• If you press the matrix button a contact matrix appears as defined in Dupuis et al "Protein secondary structure assignment through Voronoï tessellation" Proteins :  2004;55:519-528 

How to use the 3D windows in Voro3D ?

The two Cortona 3D windows presented in Voro3D were designed by Parallelgraphics. See their User's guide.