Difference between revisions of "Recycling Corner/DNA Generator"

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(Fix atomno bug with +)
(Avoid "axis," a newly reserved word)
 
(3 intermediate revisions by the same user not shown)
Line 32: Line 32:
  
 
Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.
 
Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.
<pre>##  POLYMERAZE - Jmol script by Ron Mignery
+
<pre>#  POLYMERAZE - Jmol script by Ron Mignery
#  v1.12 beta    7/21/2014 -add multi-frame support-fixed some more
+
#  v1.16 beta    4/12/2016 -axis is now a reserved word
 
#
 
#
 
#  POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
 
#  POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
Line 61: Line 61:
 
#  A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil
 
#  A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil
  
 +
kPolymeraze = 1
 
# The following constant values determine the pitch of the helices
 
# The following constant values determine the pitch of the helices
 
kC5O5PO3 = -27.0
 
kC5O5PO3 = -27.0
Line 74: Line 75:
 
gA = ""
 
gA = ""
 
gSeq = ""
 
gSeq = ""
gAppendNew = FALSE
+
gAppendNew = false
gNewFrame = FALSE
+
gNewFrame = false
  
 
# Lookup 3 letter code from 1 letter code
 
# Lookup 3 letter code from 1 letter code
Line 83: Line 84:
 
# Generate PDB atom record
 
# Generate PDB atom record
 
# Writes gNa or gNb
 
# Writes gNa or gNb
function gen_atom(atomname, group, resno, xyz, comp) {
+
function gen_atom_nt(atomname, group, resno, xyz, comp) {
 
     # Fixed column format:
 
     # Fixed column format:
 
     #ATOM    500  O4'  DA B  29      -3.745  7.211  45.474
 
     #ATOM    500  O4'  DA B  29      -3.745  7.211  45.474
Line 98: Line 99:
  
 
# Generate a PDB nucleotide record set
 
# Generate a PDB nucleotide record set
# Calls gen_atom that writes gNa or gNb
+
# Calls gen_atom_nt that writes gNa or gNb
 
function gen_nt(i, nt, rna, comp) {
 
function gen_nt(i, nt, rna, comp) {
  
Line 150: Line 151:
 
         }
 
         }
 
     }
 
     }
     var a = gen_atom(" P  ", n3, i, P0, comp)
+
     var a = gen_atom_nt(" P  ", n3, i, P0, comp)
     a += gen_atom(" OP1", n3, i, OP1, comp)
+
     a += gen_atom_nt(" OP1", n3, i, OP1, comp)
     a += gen_atom(" OP2", n3, i, OP2, comp)
+
     a += gen_atom_nt(" OP2", n3, i, OP2, comp)
     a += gen_atom(" O5'", n3, i, O5p, comp)
+
     a += gen_atom_nt(" O5'", n3, i, O5p, comp)
     a += gen_atom(" C5'", n3, i, C5p, comp)
+
     a += gen_atom_nt(" C5'", n3, i, C5p, comp)
     a += gen_atom(" C4'", n3, i, C4p, comp)
+
     a += gen_atom_nt(" C4'", n3, i, C4p, comp)
     a += gen_atom(" O4'", n3, i, O4p, comp)
+
     a += gen_atom_nt(" O4'", n3, i, O4p, comp)
     a += gen_atom(" C3'", n3, i, C3p, comp)
+
     a += gen_atom_nt(" C3'", n3, i, C3p, comp)
     a += gen_atom(" O3'", n3, i, O3p, comp)
+
     a += gen_atom_nt(" O3'", n3, i, O3p, comp)
     a += gen_atom(" C2'", n3, i, C2p, comp)
+
     a += gen_atom_nt(" C2'", n3, i, C2p, comp)
    a += gen_atom(" C1'", n3, i, C1p, comp)
 
 
     if (rna) {
 
     if (rna) {
         a += gen_atom(" O2'", n3, i, O2p, comp)
+
         a += gen_atom_nt(" O2'", n3, i, O2p, comp)
 
     }
 
     }
 +
    a += gen_atom_nt(" C1'", n3, i, C1p, comp)
  
 
     # Now add NT specific atom records
 
     # Now add NT specific atom records
 
     switch (nt) {
 
     switch (nt) {
 
     case 'A' :
 
     case 'A' :
         a += gen_atom(" N9 ", n3, i, N9ag, comp)
+
         a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
         a += gen_atom(" C8 ", n3, i, C8ag, comp)
+
         a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
         a += gen_atom(" N7 ", n3, i, N7ag, comp)
+
         a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
         a += gen_atom(" C5 ", n3, i, C5ag, comp)
+
         a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
         a += gen_atom(" C6 ", n3, i, C6ag, comp)
+
         a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
         a += gen_atom(" N6 ", n3, i, NO6ag, comp)
+
         a += gen_atom_nt(" N6 ", n3, i, NO6ag, comp)
         a += gen_atom(" N1 ", n3, i, N1ag, comp)
+
         a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
         a += gen_atom(" C2 ", n3, i, C2ag, comp)
+
         a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
         a += gen_atom(" N3 ", n3, i, N3ag, comp)
+
         a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
         a += gen_atom(" C4 ", n3, i, C4ag, comp)
+
         a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
 
         break;
 
         break;
 
     case 'C' :
 
     case 'C' :
         a += gen_atom(" N1 ", n3, i, N1ct, comp)
+
         a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
         a += gen_atom(" C2 ", n3, i, C2ct, comp)
+
         a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
         a += gen_atom(" O2 ", n3, i, O2ct, comp)
+
         a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
         a += gen_atom(" N3 ", n3, i, N3ct, comp)
+
         a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
         a += gen_atom(" C4 ", n3, i, C4ct, comp)
+
         a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
         a += gen_atom(" N4 ", n3, i, NO4ct, comp)
+
         a += gen_atom_nt(" N4 ", n3, i, NO4ct, comp)
         a += gen_atom(" C5 ", n3, i, C5ct, comp)
+
         a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
         a += gen_atom(" C6 ", n3, i, C6ct, comp)
+
         a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
 
         break;
 
         break;
 
     case 'X' :
 
     case 'X' :
 
     case 'G' :
 
     case 'G' :
         a += gen_atom(" N9 ", n3, i, N9ag, comp)
+
         a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
         a += gen_atom(" C8 ", n3, i, C8ag, comp)
+
         a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
         a += gen_atom(" N7 ", n3, i, N7ag, comp)
+
         a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
         a += gen_atom(" C5 ", n3, i, C5ag, comp)
+
         a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
         a += gen_atom(" C6 ", n3, i, C6ag, comp)
+
         a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
         a += gen_atom(" O6 ", n3, i, NO6ag, comp)
+
         a += gen_atom_nt(" O6 ", n3, i, NO6ag, comp)
         a += gen_atom(" N1 ", n3, i, N1ag, comp)
+
         a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
         a += gen_atom(" C2 ", n3, i, C2ag, comp)
+
         a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
         a += gen_atom(" N2 ", n3, i, nN2ag, comp)
+
         a += gen_atom_nt(" N2 ", n3, i, nN2ag, comp)
         a += gen_atom(" N3 ", n3, i, N3ag, comp)
+
         a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
         a += gen_atom(" C4 ", n3, i, C4ag, comp)
+
         a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
 
         break;
 
         break;
 
     case 'T' :
 
     case 'T' :
         a += gen_atom(" N1 ", n3, i, N1ct, comp)
+
         a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
         a += gen_atom(" C2 ", n3, i, C2ct, comp)
+
         a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
         a += gen_atom(" O2 ", n3, i, O2ct, comp)
+
         a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
         a += gen_atom(" N3 ", n3, i, N3ct, comp)
+
         a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
         a += gen_atom(" C4 ", n3, i, C4ct, comp)
+
         a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
         a += gen_atom(" O4 ", n3, i, NO4ct, comp)
+
         a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
         a += gen_atom(" C5 ", n3, i, C5ct, comp)
+
         a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
         a += gen_atom(" C6 ", n3, i, C6ct, comp)
+
         a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
         a += gen_atom(" C7 ", n3, i, nC7ct, comp)
+
         a += gen_atom_nt(" C7 ", n3, i, nC7ct, comp)
 
         break;
 
         break;
 
     case 'D' :
 
     case 'D' :
 
     case 'U' :
 
     case 'U' :
         a += gen_atom(" N1 ", n3, i, N1ct, comp)
+
         a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
         a += gen_atom(" C2 ", n3, i, C2ct, comp)
+
         a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
         a += gen_atom(" O2 ", n3, i, O2ct, comp)
+
         a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
         a += gen_atom(" N3 ", n3, i, N3ct, comp)
+
         a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
         a += gen_atom(" C4 ", n3, i, C4ct, comp)
+
         a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
         a += gen_atom(" O4 ", n3, i, NO4ct, comp)
+
         a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
         a += gen_atom(" C5 ", n3, i, C5ct, comp)
+
         a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
         a += gen_atom(" C6 ", n3, i, C6ct, comp)
+
         a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
 
         break;
 
         break;
 
     default :
 
     default :
Line 235: Line 236:
 
# a1 and all connected except by a2 must be selected
 
# a1 and all connected except by a2 must be selected
 
function set_angle_no (a1no, a2no, a3no, toangle) {
 
function set_angle_no (a1no, a2no, a3no, toangle) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     var c = gChain1
 
     var c = gChain1
     var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
+
     var a1 =  {(atomno=a1no) and (chain=c) and thisModel}
     var a2 =  {(atomno=a2no) and (chain=c) and (file=f) and (model=m)}
+
     var a2 =  {(atomno=a2no) and (chain=c) and thisModel}
     var a3 =  {(atomno=a3no) and (chain=c) and (file=f) and (model=m)}
+
     var a3 =  {(atomno=a3no) and (chain=c) and thisModel}
 
     var v1 = (a1.xyz - a2.xyz)
 
     var v1 = (a1.xyz - a2.xyz)
 
     var v2 = (a3.xyz - a2.xyz)
 
     var v2 = (a3.xyz - a2.xyz)
     var axis = cross(v1, v2) + a2.xyz
+
     var caxis = cross(v1, v2) + a2.xyz
 
     var curangle =  angle(a1, a2, a3)
 
     var curangle =  angle(a1, a2, a3)
     rotateselected @axis @a2 @{curangle-toangle}
+
     rotateselected @caxis @a2 @{curangle-toangle}
 
}
 
}
  
Line 252: Line 251:
 
# If selected < unselected ==> a2 < a3 and vice versa
 
# If selected < unselected ==> a2 < a3 and vice versa
 
function set_dihedral_no (a1no, a2no, a3no, a4no, toangle) {
 
function set_dihedral_no (a1no, a2no, a3no, a4no, toangle) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     var c = gChain1
 
     var c = gChain1
     var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
+
     var a1 =  {(atomno=a1no) and (chain=c) and thisModel}
     var a2 =  {(atomno=a2no) and (chain=c) and (file=f) and (model=m)}
+
     var a2 =  {(atomno=a2no) and (chain=c) and thisModel}
     var a3 =  {(atomno=a3no) and (chain=c) and (file=f) and (model=m)}
+
     var a3 =  {(atomno=a3no) and (chain=c) and thisModel}
     var a4 =  {(atomno=a4no) and (chain=c) and (file=f) and (model=m)}
+
     var a4 =  {(atomno=a4no) and (chain=c) and thisModel}
 
     var curangle =  angle(a1, a2, a3, a4)
 
     var curangle =  angle(a1, a2, a3, a4)
 
     rotateselected @a2 @a3 @{toangle-curangle}
 
     rotateselected @a2 @a3 @{toangle-curangle}
Line 281: Line 278:
 
     if (reverse) {
 
     if (reverse) {
 
         for (var i = gSeq.count; i > 0; i--) {
 
         for (var i = gSeq.count; i > 0; i--) {
             seq += gSeq[i]%9999%0
+
             if ("AUCGT".find(gSeq[i]) > 0) {
 +
                seq += gSeq[i]%9999%0
 +
            }
 +
            else {
 +
                print format("Unknown nucleotide %s!", seq[i])
 +
            }
 
         }
 
         }
 
     }
 
     }
 
     else {
 
     else {
         seq = gSeq%9999%0
+
         for (var i = 1; i <= gSeq.count; i++) {
 +
            if ("AUCGT".find(gSeq[i]) > 0) {
 +
                seq += gSeq[i]%9999%0
 +
            }
 +
            else {
 +
                print format("Unknown nucleotide %s!", seq[i])
 +
            }
 +
        }
 
     }
 
     }
  
Line 298: Line 307:
  
 
     # global new P atom index for chain A
 
     # global new P atom index for chain A
     gNa = ((m > 0) ? {(file=f) and (model=m)}.atomno.max + 1 : 1)
+
     gNa = ((m > 0) ? {thisModel}.atomno.max + 1 : 1)
 
     gNb = 0
 
     gNb = 0
 
     if (double) {
 
     if (double) {
Line 310: Line 319:
 
     gAppendNew = appendNew
 
     gAppendNew = appendNew
 
     if (gNewFrame) {
 
     if (gNewFrame) {
         appendNew = TRUE
+
         appendNew = true
 
         gNa = 1
 
         gNa = 1
 
     }
 
     }
 
     else {
 
     else {
         appendNew = FALSE
+
         appendNew = false
  
         # While there is an atom at the origin
+
         # If there is an atom at the origin
 
         while (m > 0) {
 
         while (m > 0) {
  
             var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
+
             var ai = {within(0.1, {0 0 0}) and thisModel}
             if (ai.size > 0) {
+
             if (ai) {
  
 
                 # If on the same chain
 
                 # If on the same chain
Line 328: Line 337:
 
                     echo "Adding to existing strand..."
 
                     echo "Adding to existing strand..."
 
                     pNa = ai.atomno
 
                     pNa = ai.atomno
                     aResno = {(chain=gChain1) and (file=f)
+
                     aResno = get_resno_max(gChain1) + 1
                        and (model=m)}.resno.max + 1
+
                     gNa = {(chain=gChain1) and thisModel}.atomno.max + 1
                     gNa = {(chain=gChain1) and (file=f)
 
                        and (model=m)}.atomno.max + 1
 
 
                     gNb += gNa
 
                     gNb += gNa
  
Line 338: Line 345:
 
                     gNb = aAtomCount + bAtomCount + gNa
 
                     gNb = aAtomCount + bAtomCount + gNa
 
                     gA = "data \"append nt\"\n"    # global PDB atom record
 
                     gA = "data \"append nt\"\n"    # global PDB atom record
                     for (j = 1; j <= all.atomno.max; j++) {
+
                     for (var j = 1; j <= all.atomno.max; j++) {
                         var aj = {(atomno=j) and (file=f) and (model=m)
+
                         var aj = {(atomno=j) and thisModel
 
                             and (chain == gChain2)}
 
                             and (chain == gChain2)}
                         if (aj.size > 0) {
+
                         if (aj) {
                             gA += gen_atom(aj.atomName, aj.group,
+
                             gA += gen_atom_nt(aj.atomName, aj.group,
 
                                 (aj.resno+seq.count+cSeq.count),
 
                                 (aj.resno+seq.count+cSeq.count),
 
                                 array(aj.x, aj.y, aj.z), true)
 
                                 array(aj.x, aj.y, aj.z), true)
Line 355: Line 362:
 
                 # Else move all from the new chain rightward on X axis
 
                 # Else move all from the new chain rightward on X axis
 
                 else {
 
                 else {
                     select {(file=f) and (model=m) and (chain!=gChain1)
+
                     select {thisModel and (chain!=gChain1)
 
                         and (chain!=gChain2)}
 
                         and (chain!=gChain2)}
 
                     translateselected {0, -20, -20 }
 
                     translateselected {0, -20, -20 }
Line 372: Line 379:
 
     # For each NT
 
     # For each NT
 
     for (var i = 1; i <= seq.count; i++) {
 
     for (var i = 1; i <= seq.count; i++) {
 
        if (seq[i] == "") {
 
            continue
 
        }
 
  
 
         # Move polynucleotide O3p to bond distance 1.59 from new nt P
 
         # Move polynucleotide O3p to bond distance 1.59 from new nt P
 
         var pO3 = {  -0.759, 0.925, 1.048}
 
         var pO3 = {  -0.759, 0.925, 1.048}
 
         if (double) {
 
         if (double) {
             select ((@cha or @chb) and (file=f) and (model=m))
+
             select ((@cha or @chb) and thisModel)
 
         }
 
         }
 
         else {
 
         else {
             select (@cha and (file=f) and (model=m))
+
             select (@cha and thisModel)
 
         }
 
         }
 
         if ((i + aResno) > 2) {
 
         if ((i + aResno) > 2) {
 
             var nO3 =  {@cha and (atomno=@{pNa+8})
 
             var nO3 =  {@cha and (atomno=@{pNa+8})
                 and (file=f) and (model=m)}.xyz
+
                 and thisModel}.xyz
 
             var xyz = @{pO3 - nO3}
 
             var xyz = @{pO3 - nO3}
             translateselected @xyz
+
             if (xyz) {
 +
                translateselected @xyz
 +
            }
 
         }
 
         }
  
 
         # Gen NT ==================================================
 
         # Gen NT ==================================================
 
         gA = "data \"append nt\"\n"    # global PDB atom record
 
         gA = "data \"append nt\"\n"    # global PDB atom record
         gA += gen_nt(aResno, seq[i], (drm == 1), FALSE); # gNa updated
+
         gA += gen_nt(aResno, seq[i], (drm == 1), false); # gNa updated
 
         if (double) {
 
         if (double) {
 
             nNb = gNb
 
             nNb = gNb
 
             var nti = cSeq.count-i+1
 
             var nti = cSeq.count-i+1
             gA += gen_nt(bResno, cSeq[nti], (drm > 0), TRUE); # gNb++
+
             gA += gen_nt(bResno, cSeq[nti], (drm > 0), true); # gNb++
 
             if (i > 0) {
 
             if (i > 0) {
 
                 gNb -= count_atoms(cSeq, (drm>0), nti-1, nti)
 
                 gNb -= count_atoms(cSeq, (drm>0), nti-1, nti)
Line 406: Line 411:
 
         script inline @{gA} # <== new atoms added here
 
         script inline @{gA} # <== new atoms added here
  
        f = (_frameID/1000000)
+
         appendNew = false
        m = (_frameID%1000000)
 
         appendNew = FALSE
 
  
 
         # Flip comp to comp strand
 
         # Flip comp to comp strand
 
         if (double) {
 
         if (double) {
 +
            f = (_frameID/1000000)
 +
            m = (_frameID%1000000)
 
             select @{("" + bResno + chb + "/" + f + "." + m)}
 
             select @{("" + bResno + chb + "/" + f + "." + m)}
 
             var v1={8.238, 2.809, 6.004}
 
             var v1={8.238, 2.809, 6.004}
Line 423: Line 428:
 
             # Set the angles between the new NT and the old NTs
 
             # Set the angles between the new NT and the old NTs
 
             select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
 
             select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                 and (file=f) and (model=m))
+
                 and thisModel)
 
             set_angle_no(nNa, pNa+8, pNa+7, 120.0)
 
             set_angle_no(nNa, pNa+8, pNa+7, 120.0)
 
             select (((@cha and (atomno < @{nNa+3}))
 
             select (((@cha and (atomno < @{nNa+3}))
                 or (@chb and (resno != bResno))) and (file=f) and (model=m))
+
                 or (@chb and (resno != bResno))) and thisModel)
 
             set_dihedral_no(nNa+4, nNa+3, nNa, pNa+8, kC5O5PO3)
 
             set_dihedral_no(nNa+4, nNa+3, nNa, pNa+8, kC5O5PO3)
  
 
             select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
 
             select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                 and (file=f) and (model=m))
+
                 and thisModel)
 
             set_dihedral_no(nNa+3, nNa, pNa+8, pNa+7, kO5PO3C3)
 
             set_dihedral_no(nNa+3, nNa, pNa+8, pNa+7, kO5PO3C3)
  
Line 448: Line 453:
 
     appendNew = gAppendNew
 
     appendNew = gAppendNew
 
     echo
 
     echo
     select ((file=f) and (model=m))
+
     select (thisModel)
 
     refresh
 
     refresh
  
Line 455: Line 460:
 
         script $SCRIPT_PATH$toabNT.spt
 
         script $SCRIPT_PATH$toabNT.spt
 
         var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "tight B"))
 
         var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "tight B"))
         var p = prompt(s, "Yes|No", TRUE)
+
         var p = prompt(s, "Yes|No", true)
 
         if (p = "Yes") {
 
         if (p = "Yes") {
 
             to_ab_nt_auto(gChain1, (drm > 0))
 
             to_ab_nt_auto(gChain1, (drm > 0))
Line 477: Line 482:
 
     }
 
     }
  
     var single = FALSE
+
     var single = false
     var reverse = FALSE
+
     var reverse = false
 
     var drm = 0
 
     var drm = 0
     var done = FALSE
+
     var done = false
 
     gSeq = seq%9999%0
 
     gSeq = seq%9999%0
 
     print format ("Seq=%s", gSeq)
 
     print format ("Seq=%s", gSeq)
  
     gNewFrame = FALSE
+
     gNewFrame = false
 
     if (gSeq[1] == '+') {
 
     if (gSeq[1] == '+') {
         gNewFrame = TRUE
+
         gNewFrame = true
 
         gSeq = gSeq[2][9999]
 
         gSeq = gSeq[2][9999]
 
     }
 
     }
Line 498: Line 503:
 
         gSeq = gSeq[4][9999]
 
         gSeq = gSeq[4][9999]
 
     }
 
     }
     while (done == FALSE) {
+
     while (done == false) {
         done = TRUE;
+
         done = true;
 
         if (gSeq[1] == 'S') {
 
         if (gSeq[1] == 'S') {
             single = TRUE;
+
             single = true;
             done = FALSE;
+
             done = false;
 
         }
 
         }
 
         else if (gSeq[1] == '3') {
 
         else if (gSeq[1] == '3') {
             reverse = TRUE;
+
             reverse = true;
             done = FALSE;
+
             done = false;
 
         }
 
         }
 
         else if (gSeq[1] == 'R') {
 
         else if (gSeq[1] == 'R') {
 
             drm = 1;
 
             drm = 1;
             done = FALSE;
+
             done = false;
 
         }
 
         }
 
         else if (gSeq[1] == 'M') {
 
         else if (gSeq[1] == 'M') {
 
             drm = 2;
 
             drm = 2;
             done = FALSE;
+
             done = false;
 
         }
 
         }
         if (done == FALSE) {
+
         if (done == false) {
 
             gSeq = gSeq[2][9999]
 
             gSeq = gSeq[2][9999]
 
         }
 
         }
Line 529: Line 534:
  
 
     # Generate
 
     # Generate
     gen_helix_strand(reverse, drm, single ? FALSE : TRUE)
+
     gen_helix_strand(reverse, drm, single ? false : true)
  
 
}
 
}

Latest revision as of 17:02, 12 April 2016

POLYMERAZE takes a string message encoding a nucleotide (nt) sequence and generates a corresponding double helix one nt at a time from the 5' terminus to the 3' terminus rotating the emerging helix as it goes.

The resulting polynucleotide defaults to an open B-form. If the script "to_ab_nt" described here is available, it prompts to converts to a regular B-form if DNA or to a regular A-form if RNA or mixed.

The message is a string entered by the user at a prompt. It may be typed in or pasted in and be of any length. If the first character is '+' then the polynucleotide is created in a new frame. If prepended with '3' then the string is considered as 3' to 5'. If prepended with 'R' then RNA is generated instead of DNA. If prepended with 'S' then a single strand helix is produced. If prepended with 'M' then a mixed helix is produced where the first strand is DNA and the second RNA. Multiple prepends are allowed (though 'M' would be inconsistent with 'R' or 'S').

If the 3d character is ':' (4th if the first is '+') then the two chains are labeled by the two preceding characters instead of the default 'A' and 'B'. Likewise if the 2d character is ':' then the presumably single chain is labeled by the preceding single character.

With this script you can generate a polynucleotide helix chain from a sequence string in 1-char NT coding. You can optionally give it chain labels other than the default :A :B. You can also add to an existing chain(s), add new chains to an existing model or now create the chain(s) in a new frame by prepending a '+' to the sequence string.

Chains start from the origin and extend along the -X+Y+Z axis as they are built. If a chain with the same chain label as the new chain is at the origin, the new sequence is added to the old. If a chain with a different chain label is at the origin, all existing chains are shifted 20 angstroms to the left along the YZ axis until the origin is clear.

Note that a single chain helix could then be added to a double chain or RNA to DNA or whatever. Have fun...

The IUPAC/IUBMB 1 letter code is used: A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil

The top level function plicoGenNt prompts the user for input.

The top level function plicoGenHelix accepts a string as a parameter.

Polymeraze is a member of the Plico suite of protein folding tools described here. It may be installed and accessed as a macro with the file:

Title=PLICO Generate Polynucleotide
Script=script <path to your script directory>/polymeraze.spt;plico_gen_nt

saved as plicoGenNT.macro in your .jmol/macros directory as described in Macro.

Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.

#   POLYMERAZE - Jmol script by Ron Mignery
#   v1.16 beta    4/12/2016 -axis is now a reserved word
#
#   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
#   and generates a corresponding double helix one nt at a time from the
#   5' terminus to the 3' terminus rotating the emerging helix as it goes.
#
#   The resulting polynucleotide defaults to an open B-form.  If double-stranded
#   and the script "to_ab_nt" is available, it prompts to converts to a regular
#   B-form if DNA or to a regular A-form if RNA or mixed.
#
#   The message is a string entered by the user at a prompt.
#   It may be typed in or pasted in and be of any length
#   If the 1st character is '+' then the chain is created in a new frame.
#   If prepended with '3' then the string is considered as 3' to 5'
#   If prepended with 'R' then RNA is generated instead of DNA (Ts convert to Us)
#   If prepended with 'S' then a single strand helix is produced
#   If prepended with 'M' then a mixed helix is produced where the first
#   strand is DNA and the second RNA - multiple prepends are allowed
#   though 'M' is inconsistent with 'R' or 'S'
#
#   If the 3d (4th if 1st is '+') character is ':' then the two chains are labeled
#   by the two preceding characters instead of the default 'A' and 'B'
#   Likewise if the 2d character is ':' then the presumably single chain is
#   labeled by the single preceding character
#
#   The IUPAC/IUBMB 1 letter code is used:
#   A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil

kPolymeraze = 1
# The following constant values determine the pitch of the helices
kC5O5PO3 = -27.0
kO5PO3C3 = -117.8
kPO3C3C4 = -171.9
kO3C3C4C5 = 121
kC3C4C5O5 = 54
kC4C5O5P = 164
kPu = 65
kPy = 52
gChain1 = 'A'    # The default chain id
gChain2 = 'B'    # The default complementary chain id
gA = ""
gSeq = ""
gAppendNew = false
gNewFrame = false

# Lookup 3 letter code from 1 letter code
kNt3from1 = {"A":" DA", "C":" DC", "G":" DG", "T":" DT", "U":" DU", "D":" DD", "X":" DX"}
kNtComp = {"A":"T", "C":"G", "G":"C", "T":"A", "U":"A", "D":"G", "X":"C"}

# Generate PDB atom record
# Writes gNa or gNb
function gen_atom_nt(atomname, group, resno, xyz, comp) {
    # Fixed column format:
    #ATOM    500  O4'  DA B  29      -3.745   7.211  45.474
    while (atomname.size < 3) {
        atomname += " ";
    }
    var a =  format("ATOM  %5d %4s %3s ", (comp ? gNb : gNa), atomname, group )
    a +=  format("%s%4d    %8.3f", (comp ? gChain2 : gChain1), resno, xyz[1] )
    a +=  format("%8.3f%8.3f\n", xyz[2], xyz[3] )
    if (comp) gNb++; else gNa++

    return a
};

# Generate a PDB nucleotide record set
# Calls gen_atom_nt that writes gNa or gNb
function gen_nt(i, nt, rna, comp) {

    # From constructed nucleotides
    var P0 =  [0.000, 0.000, 0.000]
    var OP1=  [-0.973,0.363,-1.067]
    var OP2=  [0.297,-1.428, 0.272]
    var O5p=  [1.351, 0.795,-0.286]
    var C5p=  [1.345, 2.211,-0.125]
    var C4p=  [2.732, 2.786,-0.255]
    var O4p=  [3.413, 2.900, 1.019]
    var C3p=  [3.670, 2.020,-1.178]
    var O3p=  [4.269, 2.960,-2.051]
    var C2p=  [4.717, 1.445,-0.238]
    var O2p=  [6.046, 1.365,-0.884]
    var C1p=  [4.758, 2.505, 0.846]

    var N1ct= [5.277, 2.056, 2.143]
    var C2ct= [6.236, 2.836, 2.740]
    var O2ct= [6.670, 3.853, 2.230]
    var N3ct= [6.674, 2.381, 3.958]
    var C4ct= [6.256, 1.245, 4.622]
    var NO4ct=[6.726, 0.972, 5.728]
    var C5ct= [5.255, 0.455, 3.924]
    var C6ct= [4.820, 0.900, 2.737]
    var nC7ct=[4.762,-0.811, 4.551]

    var N9ag= [5.256, 2.091, 2.152]
    var C8ag= [4.867, 1.016, 2.913]
    var N7ag= [5.532, 0.894, 4.035]
    var C5ag= [6.425, 1.959, 4.013]
    var C6ag= [7.401, 2.391, 4.922]
    var NO6ag=[7.656, 1.780, 6.081]
    var N1ag= [8.118, 3.493, 4.599]
    var C2ag= [7.865, 4.104, 3.438]
    var nN2ag=[8.616, 5.197, 3.181]
    var N3ag= [6.968, 3.796, 2.503]
    var C4ag= [6.271, 2.701, 2.856]

    # Build PDB atom records common to all NTs
    var n3 = kNt3from1[nt]
    if (n3 = "") {
        n3 = " D?"
    }
    if (rna) {
        if (n3 == " DD") {
            n3 = "  D"
        }
        else {
            n3 = n3.replace('D', ' ')
        }
    }
    var a = gen_atom_nt(" P  ", n3, i, P0, comp)
    a += gen_atom_nt(" OP1", n3, i, OP1, comp)
    a += gen_atom_nt(" OP2", n3, i, OP2, comp)
    a += gen_atom_nt(" O5'", n3, i, O5p, comp)
    a += gen_atom_nt(" C5'", n3, i, C5p, comp)
    a += gen_atom_nt(" C4'", n3, i, C4p, comp)
    a += gen_atom_nt(" O4'", n3, i, O4p, comp)
    a += gen_atom_nt(" C3'", n3, i, C3p, comp)
    a += gen_atom_nt(" O3'", n3, i, O3p, comp)
    a += gen_atom_nt(" C2'", n3, i, C2p, comp)
    if (rna) {
        a += gen_atom_nt(" O2'", n3, i, O2p, comp)
    }
    a += gen_atom_nt(" C1'", n3, i, C1p, comp)

    # Now add NT specific atom records
    switch (nt) {
    case 'A' :
        a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
        a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
        a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
        a += gen_atom_nt(" N6 ", n3, i, NO6ag, comp)
        a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
        break;
    case 'C' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" N4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        break;
    case 'X' :
    case 'G' :
        a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
        a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
        a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
        a += gen_atom_nt(" O6 ", n3, i, NO6ag, comp)
        a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
        a += gen_atom_nt(" N2 ", n3, i, nN2ag, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
        break;
    case 'T' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        a += gen_atom_nt(" C7 ", n3, i, nC7ct, comp)
        break;
    case 'D' :
    case 'U' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        break;
    default :
        break;
    }

    return a
};

# Rotate a1 on a2 in the plane of a1, a2 and a3 to the given angle
# a1 and all connected except by a2 must be selected
function set_angle_no (a1no, a2no, a3no, toangle) {
    var c = gChain1
    var a1 =  {(atomno=a1no) and (chain=c) and thisModel}
    var a2 =  {(atomno=a2no) and (chain=c) and thisModel}
    var a3 =  {(atomno=a3no) and (chain=c) and thisModel}
    var v1 = (a1.xyz - a2.xyz)
    var v2 = (a3.xyz - a2.xyz)
    var caxis = cross(v1, v2) + a2.xyz
    var curangle =  angle(a1, a2, a3)
    rotateselected @caxis @a2 @{curangle-toangle}
}

# Set the dihedral to the given angle
# a1 (or a4) and all connected except by a2 (or a3) must be selected
# If selected < unselected ==> a2 < a3 and vice versa
function set_dihedral_no (a1no, a2no, a3no, a4no, toangle) {
    var c = gChain1
    var a1 =  {(atomno=a1no) and (chain=c) and thisModel}
    var a2 =  {(atomno=a2no) and (chain=c) and thisModel}
    var a3 =  {(atomno=a3no) and (chain=c) and thisModel}
    var a4 =  {(atomno=a4no) and (chain=c) and thisModel}
    var curangle =  angle(a1, a2, a3, a4)
    rotateselected @a2 @a3 @{toangle-curangle}
}

function count_atoms(seq, rna, start, finish) {
    var ntc = {"A":21, "C":20, "G":22, "T":20, "U":19}
    var cnt = 0
    for (var i = start; i <= finish; i++) {
        cnt += (ntc[seq[i]] + (rna ? 1 : 0))
    }
    return cnt
}

# Generate a helix
function gen_helix_strand(reverse, drm, double) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var cha = ":" + gChain1
    var chb = ":" + gChain2
    var seq = ""
    if (reverse) {
        for (var i = gSeq.count; i > 0; i--) {
            if ("AUCGT".find(gSeq[i]) > 0) {
                seq += gSeq[i]%9999%0
            }
            else {
                print format("Unknown nucleotide %s!", seq[i])
            }
        }
    }
    else {
        for (var i = 1; i <= gSeq.count; i++) {
            if ("AUCGT".find(gSeq[i]) > 0) {
                seq += gSeq[i]%9999%0
            }
            else {
                print format("Unknown nucleotide %s!", seq[i])
            }
        }
    }

    var cSeq = ""
    if (double) {
        for (var i = seq.count; i > 0; i--) {
            cSeq += ((seq[i] == 'A') and (drm > 0)) ? "U" : kNtComp[seq[i]]
        }
    }
    var aAtomCount = count_atoms(seq, (drm == 1), 1, seq.count)
    var bAtomCount = count_atoms(cSeq, (drm > 0), 1, cSeq.count)

    # global new P atom index for chain A
    gNa = ((m > 0) ? {thisModel}.atomno.max + 1 : 1)
    gNb = 0
    if (double) {
        gNb = (aAtomCount + bAtomCount
         - count_atoms(cSeq, (drm>0), cSeq.count, cSeq.count)) # last P in cSeq
    }

    var aResno = 1
    var pNa = 1    # previous gNa

    gAppendNew = appendNew
    if (gNewFrame) {
        appendNew = true
        gNa = 1
    }
    else {
        appendNew = false

        # If there is an atom at the origin
        while (m > 0) {

            var ai = {within(0.1, {0 0 0}) and thisModel}
            if (ai) {

                # If on the same chain
                if (ai[1].chain = gChain1) {

                    # Add to existing strand
                    echo "Adding to existing strand..."
                    pNa = ai.atomno
                    aResno = get_resno_max(gChain1) + 1
                    gNa = {(chain=gChain1) and thisModel}.atomno.max + 1
                    gNb += gNa

                    # Bump up all B chain atomno and resno
                    savNb = gNb
                    gNb = aAtomCount + bAtomCount + gNa
                    gA = "data \"append nt\"\n"    # global PDB atom record
                    for (var j = 1; j <= all.atomno.max; j++) {
                        var aj = {(atomno=j) and thisModel
                            and (chain == gChain2)}
                        if (aj) {
                            gA += gen_atom_nt(aj.atomName, aj.group,
                                (aj.resno+seq.count+cSeq.count),
                                array(aj.x, aj.y, aj.z), true)
                        }
                    }
                    gA += "end \"append nt\""
                    delete @chb
                    script inline @{gA} # <== new atoms added here
                    gNb = savNb
                    break;
                }
                # Else move all from the new chain rightward on X axis
                else {
                    select {thisModel and (chain!=gChain1)
                        and (chain!=gChain2)}
                    translateselected {0, -20, -20 }
                }
            }
            else {
                break
            }
        } # endwhile
    }
    var bResno = aResno + seq.count + cSeq.count - 1

    var nNa = gNa    # new P
    var nNb = 0#bBase  # new comp P

    # For each NT
    for (var i = 1; i <= seq.count; i++) {

        # Move polynucleotide O3p to bond distance 1.59 from new nt P
        var pO3 = {  -0.759, 0.925, 1.048}
        if (double) {
            select ((@cha or @chb) and thisModel)
        }
        else {
            select (@cha and thisModel)
        }
        if ((i + aResno) > 2) {
            var nO3 =  {@cha and (atomno=@{pNa+8})
                and thisModel}.xyz
            var xyz = @{pO3 - nO3}
            if (xyz) {
                translateselected @xyz
            }
        }

        # Gen NT ==================================================
        gA = "data \"append nt\"\n"    # global PDB atom record
        gA += gen_nt(aResno, seq[i], (drm == 1), false); # gNa updated
        if (double) {
            nNb = gNb
            var nti = cSeq.count-i+1
            gA += gen_nt(bResno, cSeq[nti], (drm > 0), true); # gNb++
            if (i > 0) {
                gNb -= count_atoms(cSeq, (drm>0), nti-1, nti)
            }
        }
        gA += "end \"append nt\""
        script inline @{gA} # <== new atoms added here

        appendNew = false

        # Flip comp to comp strand
        if (double) {
            f = (_frameID/1000000)
            m = (_frameID%1000000)
            select @{("" + bResno + chb + "/" + f + "." + m)}
            var v1={8.238, 2.809, 6.004}
            var v2={8.461, 4.646, 4.125}
            rotateSelected @v2 @v1 180.0
        }

        # If any older NTs
        if ((i + aResno) > 2) {

            # Set the angles between the new NT and the old NTs
            select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                and thisModel)
            set_angle_no(nNa, pNa+8, pNa+7, 120.0)
            select (((@cha and (atomno < @{nNa+3}))
                or (@chb and (resno != bResno))) and thisModel)
            set_dihedral_no(nNa+4, nNa+3, nNa, pNa+8, kC5O5PO3)

            select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                and thisModel)
            set_dihedral_no(nNa+3, nNa, pNa+8, pNa+7, kO5PO3C3)

            set_dihedral_no(nNa, pNa+8, pNa+7, pNa+5, kPO3C3C4)
        }

        # Step new and previous N
        aResno++; bResno--
        pNa = nNa
        nNa = gNa; nNb = gNb
    }

    # Make the nucleotide bonds
    connect

    # Clean up
    appendNew = gAppendNew
    echo
    select (thisModel)
    refresh

    # Convert to A-form if RNA or mixed else B-form
    try {
        script $SCRIPT_PATH$toabNT.spt
        var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "tight B"))
        var p = prompt(s, "Yes|No", true)
        if (p = "Yes") {
            to_ab_nt_auto(gChain1, (drm > 0))
        }
    }
    catch {
    }
}

# Generate a helix or two
function plico_gen_helix(seq) {

    if (gPlicoRecord != "") {
        var g = format("show file \"%s\"", gPlicoRecord)
        var ls = script(g)
        if (ls.find("FileNotFoundException")) {
            ls = ""
        }
        ls += format("plico_gen_helix(\"%s\");", gSeq)
        write var ls @gPlicoRecord
    }

    var single = false
    var reverse = false
    var drm = 0
    var done = false
    gSeq = seq%9999%0
    print format ("Seq=%s", gSeq)

    gNewFrame = false
    if (gSeq[1] == '+') {
        gNewFrame = true
        gSeq = gSeq[2][9999]
    }
    if (gSeq[2] == ':') {
        gChain1 = gSeq[1]
        gSeq = gSeq[3][9999]
    }
    else if (gSeq[3] == ':') {
        gChain1 = gSeq[1]
        gChain2 = gSeq[2]
        gSeq = gSeq[4][9999]
    }
    while (done == false) {
        done = true;
        if (gSeq[1] == 'S') {
            single = true;
            done = false;
        }
        else if (gSeq[1] == '3') {
            reverse = true;
            done = false;
        }
        else if (gSeq[1] == 'R') {
            drm = 1;
            done = false;
        }
        else if (gSeq[1] == 'M') {
            drm = 2;
            done = false;
        }
        if (done == false) {
            gSeq = gSeq[2][9999]
        }
    }

    if (drm = 1) {
        gSeq = gSeq.replace('T', 'U')
    }
    else {
        gSeq = gSeq.replace('U', 'T')
    }

    # Generate
    gen_helix_strand(reverse, drm, single ? false : true)

}

function plico_gen_nt {
    echo Generating Nucleotide Helix

    # Get the sequence from the user
    var seq = prompt("Enter NT sequence (<+AB:3RSM>ACGTU...)", "")%9999%0
    if ((seq != "NULL") and (seq.count > 0)) {
        plico_gen_helix(seq)
    }
}
# end of polymeraze.spt

Contributors

Remig