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Protein Data Bank ( PDB ) Viewer

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PDB File Viewer 

? Juan B. Gutierrez 2002-2008 

jgutierr@math.fsu.edu 

Maplet - Windows Interface 

To execute the applet, step on any part of the next procedure and hit the Enter key.
Limitations of this application are:
+ The files this maplet program recognizes are PDB files WIHTOUT  headers. 

+ Just can be plotted the basic 20 aminoacids. For example, lines containing HOH or RET cause failure. 

+ If you prefer the traditional interface, go to the second half of this document. 

> restart: interface (warnlevel=0): with(plottools): with(StringTools): with(plots): with(Maplets[Elements]):
# +++++++++++++++++++
# MyMaplet creates a maplet window.
# Indentation is unnecessary, but hopefully helps to
# clarify syntax and the long list of parameters.
# +++++++++++++++++++
MyMaplet := Maplet
(
 'onstartup'= RunWindow('W1'),
 Window['W1']
 (
   'title'="Plot Special PDB Files",
   [
     [
       "Special PDB File:", TextField['TF1'](),
       Button
       (
             "File...",
             Action(Evaluate('TF1' = "SelectPDB"))
       )
     ],

     [
       "Initial Aminoacid:", TextField['TF2']('value'=1),
       "Final Aminoacid:", TextField['TF3']('value'=1),
       "Plot Tags:", CheckBox['TF4']('value'='true')
     ],

     [TextBox['TB1']('height'=5) ],

     Plotter['PL1'](),

     [
       Button
       (
           "Plot",
           Action(Evaluate('PL1' = PlotPDB(TF1,TF2,TF3,TF4)))
       ),
       Button
       (
           "List Aminoacids",
           Action(Evaluate('TB1' = LoadAmino(TF1)))
       ),
       Button
       (
           "End", Shutdown()
       )
     ]
   ]
 ),
 FileDialog['filPDBFile']
 (
   'onapprove' = Shutdown(['filPDBFile']),
   'oncancel' = Shutdown()     
 )
):
 
# +++++++++++++++++++
# Procedure SelectPDB
# +++++++++++++++++++
SelectPDB := proc()   
   file := Maplets[Display]( Maplet( FileDialog['FD1'](
      'onapprove' = Shutdown(['FD1']),
      'oncancel' = Shutdown()
   ) ) ):
   s := file[1]:
   t := SubstituteAll(s, "\\", "//");
end proc:

# +++++++++++++++++++
# Procedure LoadAmino
# +++++++++++++++++++
LoadAmino := proc(sFile)
   # ************************************
   # Load the protein in a data structure
   # ************************************
   lProtein := readdata(sFile,[string, integer, string, string, string, string, float, float, float, float, float, string]):
   # ******************************************************
   # Store the atom range of every aminoacid in the protein
   # ******************************************************
   sCurAmn := lProtein[1][4]:
   lCurAmn := lProtein[1][6]:
   nCurAmn := 1:
   lAminoacid := []:
   n:=0:
   for i from 1 to nops(lProtein) do
       if i < nops(lProtein) then
           sNxtAmn := lProtein[i][4]:
           lNxtAmn := lProtein[i][6]:
           if lCurAmn <> lNxtAmn then
               n := n+1:
               lAminoacid := [op(lAminoacid),[n, sCurAmn, nCurAmn, i-1]]:
               lCurAmn := lNxtAmn:
               sCurAmn := sNxtAmn:
               nCurAmn := i:
           end if:
       else
           lAminoacid := [op(lAminoacid),[n+1, sCurAmn, nCurAmn, i-1]]:
       end if:
   end do:
   lAminoacid;
end proc:

# +++++++++++++++++
# Procedure PlotPDB
# +++++++++++++++++
PlotPDB := proc(sFile, nAmnIni, nAmnEnd, bShowTags)
   # Avoid the most likely to happen error: nAmnIni > nAmnEnd
   if nAmnIni > nAmnEnd then
       newAmnEnd := nAmnIni:
   else
       newAmnEnd := nAmnEnd:
   end if:
   # ************************************
   # Load the protein in a data structure
   # ************************************
   lProtein := readdata(sFile,[string, integer, string, string, string, string, float, float, float, float, float, string]):
   # ******************************************************
   # Store the atom range of every aminoacid in the protein
   # ******************************************************
   sCurAmn := lProtein[1][4]:
   lCurAmn := lProtein[1][6]:
   nCurAmn := 1:
   lAminoacid := []:
   for i from 1 to nops(lProtein) do
       if i < nops(lProtein) then
           sNxtAmn := lProtein[i][4]:
           lNxtAmn := lProtein[i][6]:
           if lCurAmn <> lNxtAmn then
               lAminoacid := [op(lAminoacid),[sCurAmn, nCurAmn, i-1]]:
               lCurAmn := lNxtAmn:
               sCurAmn := sNxtAmn:
               nCurAmn := i:
           end if:
       else
           lAminoacid := [op(lAminoacid),[sCurAmn, nCurAmn, i-1]]:
       end if:
   end do:
   # ********************************
   # Initialize the lists for graphics
   # ********************************
   lCoordList := []:
   lLabelList := []:
   lCarbon := []:
   lOxigen := []:
   lNitrogen := []:
   lSulfur := []:
   lPolyAmn := []:
   lAminoNameList := []:
   # ******************************************************
   # Build the polygons for the aminoacids
   # ******************************************************
   for j from nAmnIni to newAmnEnd do
       i := lAminoacid[j][2]:
       k := lAminoacid[j][3]:
       PolySideChain := []:

       # W is the first atom of the next aminoacid. Used for graphic continuity
       W:=[lProtein[k+1][7],lProtein[k+1][8],lProtein[k+1][9]]:

       # The first 4 atoms are always the same for every aminoacid in the sample PDB file
       N := [lProtein[i][7],lProtein[i][8],lProtein[i][9]]:
       CA:= [lProtein[i+1][7],lProtein[i+1][8],lProtein[i+1][9]]:
       C := [lProtein[i+2][7],lProtein[i+2][8],lProtein[i+2][9]]:
       OX:= [lProtein[i+3][7],lProtein[i+3][8],lProtein[i+3][9]]:
       PolyBackbone := CURVES([N,CA,C,OX,C,W], THICKNESS(3));

       # Find the geometric center of the aminoacid and put there the three-letter name
       if k-i > 4 then
           X := sum('lProtein[l][7]','l'=i+4..k)/(k-i-3):
           Y := sum('lProtein[l][8]','l'=i+4..k)/(k-i-3):
           # A little displacement in Z needed for Asparagine
           Z := sum('lProtein[l][9]','l'=i+4..k)/(k-i-3) - 0.4:
       else
           # This is the case of the Glycine, which doesn't have a side chain
           # and Alaninie, which just have one carbon as a side chain.
           # For those two, we put the tag next to the alpha carbon.
           X := lProtein[i+1][7] + 0.3:
           Y := lProtein[i+1][8] + 0.3:
           Z := lProtein[i+1][9] + 0.3:
       end if:
       AminoGeomCentr := [X, Y, Z, lAminoacid[j][1]]:
       lAminoNameList:= [op(lAminoNameList),AminoGeomCentr]:

       # ******************************************************
       # Aliphatic aminoacids (1-4)
       # ******************************************************
       # 1) A = ALA = Alanine
       if lProtein[i][4] = "ALA" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           PolySideChain := CURVES([CA,CB]);
       end if:
       # 2) V = VAL = Valine
       if lProtein[i][4] = "VAL" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,CG1]);
       end if:
       # 3) L = LEU = Leucine
       if lProtein[i][4] = "LEU" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CG,CD2]);
       end if:
       # 4) I = ILE = Isoleucine
       if lProtein[i][4] = "ILE" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,CG1,CD1]);
       end if:
       # ******************************************************
       # Hydrophobic-aromatic aminoacids (5-7)
       # ******************************************************
       # 5) F = PHE = Phenylanaline
       if lProtein[i][4] = "PHE" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CZ:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CE1,CZ,CE2,CD2,CG]);
       end if:
       # 6) Y = TYR = Tyrosine
       if lProtein[i][4] = "TYR" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CZ:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           OH:=[lProtein[i+11][7],lProtein[i+11][8],lProtein[i+11][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CE1,CZ,OH,CZ,CE2,CD2,CG]);
       end if:
       # 7) W = TRP = Tryptophan
       if lProtein[i][4] = "TRP" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CE3:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           CZ2:=[lProtein[i+11][7],lProtein[i+11][8],lProtein[i+11][9]]:
           CZ3:=[lProtein[i+12][7],lProtein[i+12][8],lProtein[i+12][9]]:
           CH2:=[lProtein[i+13][7],lProtein[i+13][8],lProtein[i+13][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,NE1,CE2,CZ2,CH2,CZ3,CE3,CD2,CE2,CD2,CG]);
       end if:
       # ******************************************************
       # Neutral-polar aminoacids (8-13)
       # ******************************************************
       # 8) S = SER = Serine
       if lProtein[i][4] = "SER" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           OG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           PolySideChain := CURVES([CA,CB,OG]);
       end if:
       # 9) T = THR = Threionine
       if lProtein[i][4] = "THR" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           OG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,OG1]);
       end if:
       # 10) C = CYS = Cysteine
       if lProtein[i][4] = "CYS" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           SG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           PolySideChain := CURVES([CA,CB,SG]);
       end if:
       # 11) M = MET = Methionine
       if lProtein[i][4] = "MET" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           SD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CE:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,SD,CE]);
       end if:
       # 12) N = ASN = Asparagine
       if lProtein[i][4] = "ASN" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           OD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           ND2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,OD1,CG,ND2]);
       end if:
       # 13) Q = GLN = Glutamine
       if lProtein[i][4] = "GLN" then
           CB := [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OE1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NE2:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,OE1,CD,NE2]);
       end if:
       # ******************************************************
       # Aliphatic aminoacids (14-15)
       # ******************************************************
       # 14) D = ASP = Aspartate
       if lProtein[i][4] = "ASP" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           OD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,OD1,CG,OD2]);
       end if:
       # 15) E = GLU = Glutamate
       if lProtein[i][4] = "GLU" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OE1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           OE2:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,OE1,CD,OE2]);
       end if:
       # ******************************************************
       # Basic aminoacids (16-18)
       # ******************************************************
       # 16) H = HIS = Histidine
       if lProtein[i][4] = "HIS" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           ND1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           NE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           PolySideChain := CURVES([CA,CB,CG,ND1,CE1,NE2,CD2,CG]);
       end if:
       # 17) K = LYS = Lysine
       if lProtein[i][4] = "LYS" then
           CB:=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CE:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NZ:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,CE,NZ]);
       end if:
       # 18) R = ARG = Arginine
       if lProtein[i][4] = "ARG" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           NE :=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CZ :=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           NH1:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           NH2:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,NE,CZ,NH1,CZ,NH2]);
       end if:
       # ******************************************************
       # Conformationally important aminoacids (19-20)
       # ******************************************************
       # 19) G = GLY = Glycine
       if lProtein[i][4] = "GLY" then
           # Glycine doesn't have a side chain
       end if:
       # 20) P = PRO = Proline
       if lProtein[i][4] = "PRO" then
           CB:=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,N]);
       end if:

       # Add sidechain, backbone and aminoacid name to the list of itme sto be plotted
       if nops(PolySideChain) > 0 then
           lPolyAmn := [op(lPolyAmn),PolySideChain]:
       end if:
       lPolyAmn := [op(lPolyAmn),PolyBackbone]:
   end do:

   # ******************************************************************************
   # Draw the atom's number and solids of different colors depending upon the atoms
   # ******************************************************************************
   for i from lAminoacid[nAmnIni][2] to lAminoacid[newAmnEnd][3] do
       lCoord := [lProtein[i][7], lProtein[i][8], lProtein[i][9]]:
       lLabel := [lProtein[i][7], lProtein[i][8], lProtein[i][9]+0.4, lProtein[i][3]]:
       if lProtein[i][12] = "C" then
           lCarbon := [op(lCarbon),lCoord]:
       end if:  
       if lProtein[i][12] = "O" then
           lOxigen := [op(lOxigen),lCoord]:
       end if:  
       if lProtein[i][12] = "N" then
           lNitrogen := [op(lNitrogen),lCoord]:
       end if:  
       if lProtein[i][12] = "S" then
           lSulfur := [op(lSulfur),lCoord]:
       end if:  
       lCoordList := [op(lCoordList),lCoord]:
       lLabelList := [op(lLabelList),lLabel]:   
   end do:

   # ******************************************************
   # Load all the objects into the PLO3D structure
   # ******************************************************
   polCarbon:=polyhedraplot(lCarbon,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=gray):
   polOxygen:=polyhedraplot(lOxigen,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=red):
   polNitrogen:=polyhedraplot(lNitrogen,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=blue):
   AtomLabel := textplot3d(lLabelList,color=black):
   AminoLabel := textplot3d(lAminoNameList,color=red):
   lSideChains := PolySideChains(lAminoacid):
   if nops(lSulfur) > 0 then
       polSulfur:=polyhedraplot(lSulfur, polytype=hexahedron,
          polyscale=0.3, lightmodel=light4, shading=XYZ,
          style=PATCHNOGRID, color=yellow):
       if bShowTags = 'true' then
           display3d(lPolyAmn, AtomLabel, AminoLabel, polCarbon,
              polOxygen, polNitrogen, polSulfur, color=black);
       else         
           display3d(lPolyAmn, polCarbon, polOxygen, polNitrogen, polSulfur, color=black);
       end if:
   else
       if bShowTags = 'true' then
           display3d(lPolyAmn, AtomLabel, AminoLabel, polCarbon,
              polOxygen, polNitrogen, color=black);
       else         
           display3d(lPolyAmn, polCarbon, polOxygen, polNitrogen, color=black);
       end if:
   end if:
end proc:

Maplets[Display](MyMaplet);
 

>  
 

Plot - Traditional Interface 

To execute the procedure, step on the line just below that begins with "restart..." and hit enter three times.
The paramters are: 

PlotPDB (FileName (string), InitialAminacid (integer), FinalAminoacid (integer), ShowTags (boolean))
Limitations of this application are:
+ The files this program recognizes are PDB files WIHTOUT  headers. 

+ Just can be plotted the basic 20 aminoacids. For example, lines containing HOH or RET cause failure. 

> restart: interface (warnlevel=0): with(plottools): with(plots):
 

> # +++++++++++++++++
# Procedure PlotPDB
# +++++++++++++++++
PlotPDB := proc(sFile, nAmnIni, nAmnEnd, bShowTags)
   # Avoid the most likely to happen error: nAmnIni > nAmnEnd
   if nAmnIni > nAmnEnd then
       newAmnEnd := nAmnIni:
   else
       newAmnEnd := nAmnEnd:
   end if:
   # ************************************
   # Load the protein in a data structure
   # ************************************
   lProtein := readdata(sFile,[string, integer, string, string, string, string, float, float, float, float, float, string]):
   # ******************************************************
   # Store the atom range of every aminoacid in the protein
   # ******************************************************
   sCurAmn := lProtein[1][4]:
   lCurAmn := lProtein[1][6]:
   nCurAmn := 1:
   lAminoacid := []:
   for i from 1 to nops(lProtein) do
       if i < nops(lProtein) then
           sNxtAmn := lProtein[i][4]:
           lNxtAmn := lProtein[i][6]:
           if lCurAmn <> lNxtAmn then
               lAminoacid := [op(lAminoacid),[sCurAmn, nCurAmn, i-1]]:
               lCurAmn := lNxtAmn:
               sCurAmn := sNxtAmn:
               nCurAmn := i:
           end if:
       else
           lAminoacid := [op(lAminoacid),[sCurAmn, nCurAmn, i-1]]:
       end if:
   end do:
   # ********************************
   # Initialize the lists for graphics
   # ********************************
   lCoordList := []:
   lLabelList := []:
   lCarbon := []:
   lOxigen := []:
   lNitrogen := []:
   lSulfur := []:
   lPolyAmn := []:
   lAminoNameList := []:
   # ******************************************************
   # Build the polygons for the aminoacids
   # ******************************************************
   for j from nAmnIni to newAmnEnd do
       i := lAminoacid[j][2]:
       k := lAminoacid[j][3]:
       PolySideChain := []:

       # W is the first atom of the next aminoacid. Used for graphic continuity
       W:=[lProtein[k+1][7],lProtein[k+1][8],lProtein[k+1][9]]:

       # The first 4 atoms are always the same for every aminoacid in the sample PDB file
       N := [lProtein[i][7],lProtein[i][8],lProtein[i][9]]:
       CA:= [lProtein[i+1][7],lProtein[i+1][8],lProtein[i+1][9]]:
       C := [lProtein[i+2][7],lProtein[i+2][8],lProtein[i+2][9]]:
       OX:= [lProtein[i+3][7],lProtein[i+3][8],lProtein[i+3][9]]:
       PolyBackbone := CURVES([N,CA,C,OX,C,W], THICKNESS(3));

       # Find the geometric center of the aminoacid and put there the three-letter name
       if k-i > 4 then
           X := sum('lProtein[l][7]','l'=i+4..k)/(k-i-3):
           Y := sum('lProtein[l][8]','l'=i+4..k)/(k-i-3):
           # A little displacement in Z needed for Asparagine
           Z := sum('lProtein[l][9]','l'=i+4..k)/(k-i-3) - 0.4:
       else
           # This is the case of the Glycine, which doesn't have a side chain
           # and Alaninie, which just have one carbon as a side chain.
           # For those two, we put the tag next to the alpha carbon.
           X := lProtein[i+1][7] + 0.3:
           Y := lProtein[i+1][8] + 0.3:
           Z := lProtein[i+1][9] + 0.3:
       end if:
       AminoGeomCentr := [X, Y, Z, lAminoacid[j][1]]:
       lAminoNameList:= [op(lAminoNameList),AminoGeomCentr]:

       # ******************************************************
       # Aliphatic aminoacids (1-4)
       # ******************************************************
       # 1) A = ALA = Alanine
       if lProtein[i][4] = "ALA" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           PolySideChain := CURVES([CA,CB]);
       end if:
       # 2) V = VAL = Valine
       if lProtein[i][4] = "VAL" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,CG1]);
       end if:
       # 3) L = LEU = Leucine
       if lProtein[i][4] = "LEU" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CG,CD2]);
       end if:
       # 4) I = ILE = Isoleucine
       if lProtein[i][4] = "ILE" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,CG1,CD1]);
       end if:
       # ******************************************************
       # Hydrophobic-aromatic aminoacids (5-7)
       # ******************************************************
       # 5) F = PHE = Phenylanaline
       if lProtein[i][4] = "PHE" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CZ:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CE1,CZ,CE2,CD2,CG]);
       end if:
       # 6) Y = TYR = Tyrosine
       if lProtein[i][4] = "TYR" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CZ:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           OH:=[lProtein[i+11][7],lProtein[i+11][8],lProtein[i+11][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,CE1,CZ,OH,CZ,CE2,CD2,CG]);
       end if:
       # 7) W = TRP = Tryptophan
       if lProtein[i][4] = "TRP" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           CE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           CE3:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           CZ2:=[lProtein[i+11][7],lProtein[i+11][8],lProtein[i+11][9]]:
           CZ3:=[lProtein[i+12][7],lProtein[i+12][8],lProtein[i+12][9]]:
           CH2:=[lProtein[i+13][7],lProtein[i+13][8],lProtein[i+13][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD1,NE1,CE2,CZ2,CH2,CZ3,CE3,CD2,CE2,CD2,CG]);
       end if:
       # ******************************************************
       # Neutral-polar aminoacids (8-13)
       # ******************************************************
       # 8) S = SER = Serine
       if lProtein[i][4] = "SER" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           OG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           PolySideChain := CURVES([CA,CB,OG]);
       end if:
       # 9) T = THR = Threionine
       if lProtein[i][4] = "THR" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           OG1:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CG2:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG2,CB,OG1]);
       end if:
       # 10) C = CYS = Cysteine
       if lProtein[i][4] = "CYS" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           SG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           PolySideChain := CURVES([CA,CB,SG]);
       end if:
       # 11) M = MET = Methionine
       if lProtein[i][4] = "MET" then
           CB:= [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           SD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CE:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,SD,CE]);
       end if:
       # 12) N = ASN = Asparagine
       if lProtein[i][4] = "ASN" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           OD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           ND2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,OD1,CG,ND2]);
       end if:
       # 13) Q = GLN = Glutamine
       if lProtein[i][4] = "GLN" then
           CB := [lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OE1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NE2:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,OE1,CD,NE2]);
       end if:
       # ******************************************************
       # Aliphatic aminoacids (14-15)
       # ******************************************************
       # 14) D = ASP = Aspartate
       if lProtein[i][4] = "ASP" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           OD1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           PolySideChain := CURVES([CA,CB,CG,OD1,CG,OD2]);
       end if:
       # 15) E = GLU = Glutamate
       if lProtein[i][4] = "GLU" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           OE1:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           OE2:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,OE1,CD,OE2]);
       end if:
       # ******************************************************
       # Basic aminoacids (16-18)
       # ******************************************************
       # 16) H = HIS = Histidine
       if lProtein[i][4] = "HIS" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           ND1:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CD2:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CE1:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           NE2:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           PolySideChain := CURVES([CA,CB,CG,ND1,CE1,NE2,CD2,CG]);
       end if:
       # 17) K = LYS = Lysine
       if lProtein[i][4] = "LYS" then
           CB:=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           CE:=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           NZ:=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,CE,NZ]);
       end if:
       # 18) R = ARG = Arginine
       if lProtein[i][4] = "ARG" then
           CB :=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG :=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD :=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           NE :=[lProtein[i+7][7],lProtein[i+7][8],lProtein[i+7][9]]:
           CZ :=[lProtein[i+8][7],lProtein[i+8][8],lProtein[i+8][9]]:
           NH1:=[lProtein[i+9][7],lProtein[i+9][8],lProtein[i+9][9]]:
           NH2:=[lProtein[i+10][7],lProtein[i+10][8],lProtein[i+10][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,NE,CZ,NH1,CZ,NH2]);
       end if:
       # ******************************************************
       # Conformationally important aminoacids (19-20)
       # ******************************************************
       # 19) G = GLY = Glycine
       if lProtein[i][4] = "GLY" then
           # Glycine doesn't have a side chain
       end if:
       # 20) P = PRO = Proline
       if lProtein[i][4] = "PRO" then
           CB:=[lProtein[i+4][7],lProtein[i+4][8],lProtein[i+4][9]]:
           CG:=[lProtein[i+5][7],lProtein[i+5][8],lProtein[i+5][9]]:
           CD:=[lProtein[i+6][7],lProtein[i+6][8],lProtein[i+6][9]]:
           PolySideChain := CURVES([CA,CB,CG,CD,N]);
       end if:

       # Add sidechain, backbone and aminoacid name to the list of itme sto be plotted
       if nops(PolySideChain) > 0 then
           lPolyAmn := [op(lPolyAmn),PolySideChain]:
       end if:
       lPolyAmn := [op(lPolyAmn),PolyBackbone]:
   end do:

   # ******************************************************************************
   # Draw the atom's number and solids of different colors depending upon the atoms
   # ******************************************************************************
   for i from lAminoacid[nAmnIni][2] to lAminoacid[newAmnEnd][3] do
       lCoord := [lProtein[i][7], lProtein[i][8], lProtein[i][9]]:
       lLabel := [lProtein[i][7], lProtein[i][8], lProtein[i][9]+0.4, lProtein[i][3]]:
       if lProtein[i][12] = "C" then
           lCarbon := [op(lCarbon),lCoord]:
       end if:  
       if lProtein[i][12] = "O" then
           lOxigen := [op(lOxigen),lCoord]:
       end if:  
       if lProtein[i][12] = "N" then
           lNitrogen := [op(lNitrogen),lCoord]:
       end if:  
       if lProtein[i][12] = "S" then
           lSulfur := [op(lSulfur),lCoord]:
       end if:  
       lCoordList := [op(lCoordList),lCoord]:
       lLabelList := [op(lLabelList),lLabel]:   
   end do:

   # ******************************************************
   # Load all the objects into the PLO3D structure
   # ******************************************************
   polCarbon:=polyhedraplot(lCarbon,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=gray):
   polOxygen:=polyhedraplot(lOxigen,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=red):
   polNitrogen:=polyhedraplot(lNitrogen,polytype=hexahedron,polyscale =0.2,lightmodel=light4,shading=XYZ,style=PATCHNOGRID,color=blue):
   AtomLabel := textplot3d(lLabelList,color=black):
   AminoLabel := textplot3d(lAminoNameList,color=red):
   lSideChains := PolySideChains(lAminoacid):
   if nops(lSulfur) > 0 then
       polSulfur:=polyhedraplot(lSulfur, polytype=hexahedron,
          polyscale=0.3, lightmodel=light4, shading=XYZ,
          style=PATCHNOGRID, color=yellow):
       if bShowTags = 'true' then
           display3d(lPolyAmn, AtomLabel, AminoLabel, polCarbon,
              polOxygen, polNitrogen, polSulfur, color=black);
       else         
           display3d(lPolyAmn, polCarbon, polOxygen, polNitrogen, polSulfur, color=black);
       end if:
   else
       if bShowTags = 'true' then
           display3d(lPolyAmn, AtomLabel, AminoLabel, polCarbon,
              polOxygen, polNitrogen, color=black);
       else         
           display3d(lPolyAmn, polCarbon, polOxygen, polNitrogen, color=black);
       end if:
   end if:

end proc:
 

> # PlotPDB (sFile, nAmnIni, nAmnEnd, bShowTags); bShowTags = 'true' or 'false'
PlotPDB ("1E0P.TXT", 1,5,'true');
 

Plot_2d  
 

>