User:Remig/plico/toABnt
ToABnt allows the user to convert a polynucleotide chain from A-form to B-form and vice versa. When you ALT-CLICK on any atom, you are prompted to convert its chain from its current form to either the A-form or the B-form. The two forms differ primarily in the pucker conformation of their sugar moieties. The A-form has its sugars in the C3'-endo conformation whereas the B-form has it in the C2'-endo conformation. The A-form is characteristic of RNA while the B-form is characteristic of DNA.
This routine is called automatically by the Plico routine Polymeraze when a polynucleotide is generated.
ToABnt 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 toAB NT Script=script <path to your script folder>/toABnt.spt;plicotoABnt
saved as toABnt.macro in your .jmol/macros folder as described in Macro.
Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
# toABnt - Jmol script by Ron Mignery # v1.0 beta 3/28/2014 for Jmol 14 # # Convert a polynucleotide chain from A-form to B-form or vice versa # var kC5O5PO3B = -71.0 var kO5PO3C3B = -106.50 var kPO3C3C4B = -160.67 var kO3C3C4C5B = 125.44 var kC3C4C5O5B = 55.65 var kC4C5O5PB = 169.10 var kO4C4C3C2B = 15.92 var kC4O4C1C2B = -41.7 var kC4O4C1NxB = -159.03 var kC5C4O4C1B = 146.31 var kC3C1C2O2B = -167.9 var kPuB = 59.0 var kPyB = 61.0 var kC5O5PO3A = -59.3 var kO5PO3C3A = -56.9 var kPO3C3C4A = -157.4 var kO3C3C4C5A = 75.5 var kC3C4C5O5A = 49.55 var kC4C5O5PA = 170.8 var kO4C4C3C2A = -35.55 var kC4O4C1C2A = 3.8 var kC4O4C1NxA = -117.4 var kC5C4O4C1A = 144.85 var kC3C1C2O2A = 116.3 var kPuA = 15 var kPyA = 15 var gToab = FALSE var gToabAlt = FALSE var gToA = FALSE kO3C3C2O2A = 42.2 # 1ana + O # 1tna=47.3 kO3C3C2O2B = -32.0 # 1bna + O function getInterbaseRotors(stator, mover) { var rotors = array() var sRes = stator.resno var mRes = mover.resno var iChain = mover.chain var mC4 = {(resno=mRes) and (chain=iChain) and (atomName="C4\'")} var mC3 = {(resno=mRes) and (chain=iChain) and (atomName="C3\'")} var mO3 = {(resno=mRes) and (chain=iChain) and (atomName="O3\'")} var sP = {(resno=sRes) and (chain=iChain) and (atomName="P")} var sO5 = {(resno=sRes) and (chain=iChain) and (atomName="O5\'")} var sC5 = {(resno=sRes) and (chain=iChain) and (atomName="C5\'")} var sC4 = {(resno=sRes) and (chain=iChain) and (atomName="C4\'")} var sC3 = {(resno=sRes) and (chain=iChain) and (atomName="C3\'")} rotors += [mC4.atomIndex, mC3.atomIndex, mO3.atomIndex, sP.atomIndex] rotors += [mC3.atomIndex, mO3.atomIndex, sP.atomIndex, sO5.atomIndex] rotors += [mO3.atomIndex, sP.atomIndex, sO5.atomIndex, sC5.atomIndex] rotors += [sP.atomIndex, sO5.atomIndex, sC5.atomIndex, sC4.atomIndex] rotors = [sO5.atomIndex, sC5.atomIndex, sC4.atomIndex, sC3.atomIndex] return rotors } function setResidueDistance(stator, mover, dist) { var selsave = {selected} var cp = mover.xyz select mover setDistanceAtoms(stator, mover, dist) var pt = mover.xyz mover.xyz = cp select selsave var rotors = getInterbaseRotors(stator, mover) toabTrackIdx(mover.atomIndex, pt, rotors) toabTrackIdx(mover.atomIndex, pt, rotors) toabTrackIdx(mover.atomIndex, pt, rotors) } # Rotate rotor set to move target atom to its proper place function toabTrackIdx(targetIdx, targetPt, iRotors) { gOK = FALSE var pt = targetPt var dist = distance(pt, {atomIndex=targetIdx}.xyz) var baseSet = {selected} var rotors = iRotors # For a number of passes for (var pass1 = 0; pass1 < 20; pass1++) { var blocked = ({}) for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) { var v1 = {atomIndex=targetIdx}.xyz - pt # Find the most orthgonal unused rotor var imax = 0 var smax = 0.5 for (var ri = 1; ri < rotors.size; ri += 4) { var i2 = rotors[ri+1] var i3 = rotors[ri+2] var i4 = rotors[ri+3] if ((i2 != targetIdx) and (i3 != targetIdx) and (i4 != targetIdx)) { if ({blocked and {atomIndex=i2}}.count == 0) { var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz var s = sin(abs(angle(v1, {0 0 0}, v2))) if (s > smax) { smax = s imax = ri } } } } # If no more rotors, break to next full try if (imax == 0) { break } var i1 = rotors[imax+0] var i2 = rotors[imax+1] var i3 = rotors[imax+2] var i4 = rotors[imax+3] # Get dihedral of rotor with target point var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt) # Add rotor stators to select select baseSet for (var ri = 1; ri <= imax; ri += 4) { {atomIndex=@{rotors[ri]}}.selected = TRUE {atomIndex=@{rotors[ri+1]}}.selected = TRUE } # Rotate to minimize vector ==================== rotateSelected {atomIndex=i2} {atomIndex=i3} @dt # If close enough, stop if (distance(pt, {atomIndex=targetIdx}) < (kDtolerance/4)) { gOK = TRUE gTargetPt = pt break } # Block rotor blocked |= {atomIndex=i2} } # endfor num rotors passes if (gOK) { break } } # endfor 20 passes } function toabNtAuto(iChain, toA) { # Load common functions if not already if (kCommon < 1) { script $SCRIPT_PATH$plicoCommon.spt if (kCommon < 1) { prompt ("A newer version of plicoCommon.SPT is required") quit } } gChain1 = iChain gToA = toA toabNt(TRUE) } function toabNt(auto) { select all g5cargoIdx = {(atomno=@{{chain=gChain1}.atomno.min}) and (chain=gChain1)}.atomIndex g3cargoIdx = {(atomno=@{{chain=gChain1}.atomno.max}) and (chain=gChain1)}.atomIndex # If new drag if (gNewDrag) { gNewDrag = FALSE save state gState } # Move the cargo select {gCargoSet} gChain1 = {atomIndex=g3cargoIdx}.chain gChain2 = "" # Move between A-form and B-form var res5 = {atomIndex=g5cargoIdx}.resno var res3 = {atomIndex=g3cargoIdx}.resno var pSet = ({}) var bSet = ({}) var k = -1 var ang = 0 var pang = 0 var isP = FALSE for (var i = res5; i <= res3; i++) { var j = i-1 var aO3 = {(resno=i) and (chain=gChain1) and (atomName="O3\'")} var aC3 = {(resno=i) and (chain=gChain1) and (atomName="C3\'")} var aC4 = {(resno=i) and (chain=gChain1) and (atomName="C4\'")} var aC5 = {(resno=i) and (chain=gChain1) and (atomName="C5\'")} var aO5 = {(resno=i) and (chain=gChain1) and (atomName="O5\'")} var aP = {(resno=i) and (chain=gChain1) and (atomName="P")} if (i == res5) { if (auto == FALSE) { isForm = "A" if (angle(aO3, aC3, aC4, aC5) > ((kO3C3C4C5A + kO3C3C4C5B)/2)) { isForm = "B" } p = prompt(format("Convert chain %s from %s-form to:", gChain1, isForm), "A-form|B-form", TRUE) if (p == "A-form") { gToA = TRUE } else if (p == "B-form") { gToA = FALSE } else { color {all} @gScheme break } print format("Converting to %s", p) } # If paired lcAtoms = (within(3.0, FALSE, {(resno=i) and (chain=gChain1) and base}) and not {chain=gChain1}) isP = (lcAtoms.size > 0) gChain2 = (isP ? lcAtoms[1].chain : "") k = (isP ? lcAtoms[1].resno : -1) } pSet = {(resno=k) and (chain=gChain2)} var bO3 = {(resno=k) and (chain=gChain2) and (atomName="O3\'")} var bC3 = {(resno=k) and (chain=gChain2) and (atomName="C3\'")} var bC4 = {(resno=k) and (chain=gChain2) and (atomName="C4\'")} var bC5 = {(resno=k) and (chain=gChain2) and (atomName="C5\'")} var bO5 = {(resno=k) and (chain=gChain2) and (atomName="O5\'")} var bP = {(resno=k) and (chain=gChain2) and (atomName="P")} # If not 5' terminus var aC4p = ({}) var aC3p = ({}) var aO3p = ({}) var bO5p = ({}) var bC4p = ({}) var bC3p = ({}) var bO3p = ({}) var bPp = ({}) if (i > res5) { aC4p = {(resno=j) and (chain=gChain1) and (atomName="C4\'")} aC3p = {(resno=j) and (chain=gChain1) and (atomName="C3\'")} aO3p = {(resno=j) and (chain=gChain1) and (atomName="O3\'")} bO5p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="O5\'")} bC4p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="C4\'")} bC3p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="C3\'")} bO3p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="O3\'")} bPp = {(resno=@{k+1}) and (chain=gChain2) and (atomName="P")} select bSet or {(atomno < @{aP.atomno}) and (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)} setDihedralAtoms(aP, aO3p, aC3p, aC4p, (gToA ? kPO3C3C4A : kPO3C3C4B)) setDihedralAtoms(aO5, aP, aO3p, aC3p, (gToA ? kO5PO3C3A : kO5PO3C3B)) select bSet or {(atomno < @{aO5.atomno}) and (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)} setDihedralAtoms(aC5, aO5, aP, aO3p, (gToA ? kC5O5PO3A : kC5O5PO3B)) } select bSet or {(atomno < @{aO5.atomno}) and (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)} setDihedralAtoms(aC4, aC5, aO5, aP, (gToA ? kC4C5O5PA : kC4C5O5PB)) select (bP or (connected(bP) and {resno=k})) setDihedralAtoms(bC4, bC5, bO5, bP, (gToA ? kC4C5O5PA : kC4C5O5PB)) select bSet or {(atomno < @{aC5.atomno}) and (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)} setDihedralAtoms(aC3, aC4, aC5, aO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B)) select (bP or (connected(bP) and {resno=k})) setDihedralAtoms(bC3, bC4, bC5, bO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B)) select (({(resno >= k) and (chain=gChain2)} or {(resno <= i) and (chain=gChain1)}) and not aO3) setDihedralAtoms(aO3, aC3, aC4, aC5, (gToA ? kO3C3C4C5A : kO3C3C4C5B)) select bO3 setDihedralAtoms(bC5, bC4, bC3, bO3, (gToA ? kO3C3C4C5A : kO3C3C4C5B)) var aC1 = {(resno=i) and (chain=gChain1) and (atomName="C1\'")} var aC2 = {(resno=i) and (chain=gChain1) and (atomName="C2\'")} var aO2 = {(resno=i) and (chain=gChain1) and (atomName="O2\'")} var aO4 = {(resno=i) and (chain=gChain1) and (atomName="O4\'")} var bC1 = {(resno=k) and (chain=gChain2) and (atomName="C1\'")} var bC2 = {(resno=k) and (chain=gChain2) and (atomName="C2\'")} var bO2 = {(resno=k) and (chain=gChain2) and (atomName="O2\'")} var bO4 = {(resno=k) and (chain=gChain2) and (atomName="O4\'")} # Set chi var aNx = -1 var aCx = -1 var bNx = -1 var bCx = -1 if ((aC1 and {purine}).size > 0) { aNx = {(resno=i) and (chain=gChain1) and (atomName="N9")} aCx = {(resno=i) and (chain=gChain1) and (atomName="C8")} bNx = {(resno=k) and (chain=gChain2) and (atomName="N1")} bCx = {(resno=k) and (chain=gChain2) and (atomName="C6")} ang = (gToA ? kPuA : kPuB) pang = (gToA ? kPyA : kPyB) } else { aNx = {(resno=i) and (chain=gChain1) and (atomName="N1")} aCx = {(resno=i) and (chain=gChain1) and (atomName="C6")} bNx = {(resno=k) and (chain=gChain2) and (atomName="N9")} bCx = {(resno=k) and (chain=gChain2) and (atomName="C8")} ang = (gToA ? kPyA : kPyB) pang = (gToA ? kPuA : kPuB) } select pSet or {(resno=i) and (chain=gChain1) and base} setDihedralAtoms(aO4, aC1, aNx, aCx, ang) select {pSet and not base} setDihedralAtoms(bCx, bNx, bC1, bO4, pang) # Set pucker 3' endo or 2' endo select pSet or {(resno=i) and (chain=gChain1) and base} setDihedralAtoms(aC4, aO4, aC1, aNx, (gToA ? kC4O4C1NxA : kC4O4C1NxB)) select {pSet and not base} setDihedralAtoms(bNx, bC1, bO4, bC4, (gToA ? kC4O4C1NxA : kC4O4C1NxB)) select (pSet or {((resno=i) and (chain=gChain1) and base) or aC1}) setDihedralAtoms(aC5, aC4, aO4, aC1, (gToA ? kC5C4O4C1A : kC5C4O4C1B)) select {pSet and not base and not bC1} setDihedralAtoms(bC1, bO4, bC4, bC5, (gToA ? kC5C4O4C1A : kC5C4O4C1B)) select aC2 or aO2 setDihedralAtoms(aC4, aO4, aC1, aC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B)) if (aO2.size > 0) { ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B) setDihedralAtoms(aC3, aC1, aC2, aO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B)) } setDistanceAtoms(aC3, aC2, 1.52) setDistanceAtoms(aC1, aC2, 1.52) select bC2 or bO2 setDihedralAtoms(bC4, bO4, bC1, bC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B)) if (bO2.size > 0) { ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B) setDihedralAtoms(bC3, bC1, bC2, bO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B)) } setDistanceAtoms(bC3, bC2, 1.52) setDistanceAtoms(bC1, bC2, 1.52) # compress if (i > res5) { select ({resno<i} or {resno>k}) and not aP #setResidueDistance(aC4, aC4p, 4.0) } # If paired, make minor adjustments if (isP and (i > res5)) { var cp = bPp.xyz select bPp setDistanceAtoms(bO3, bPp, 1.59) setAngleAtoms(bC3, bO3, bPp, 118.2) setDihedralAtoms(bC4, bC3, bO3, bPp, (gToA ? kPO3C3C4A : kPO3C3C4B)) var pt = bPp.xyz bPp.xyz = cp rotors = [aC4p.atomIndex, aC3p.atomIndex, aO3p.atomIndex, aP.atomIndex] rotors += [aC3p.atomIndex, aO3p.atomIndex, aP.atomIndex, aO5.atomIndex] rotors += [aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, aC5.atomIndex] rotors += [aP.atomIndex, aO5.atomIndex, aC5.atomIndex, aC4.atomIndex] rotors += [aO5.atomIndex, aC5.atomIndex, aC4.atomIndex, aC3.atomIndex] select ({((resno < i) and (chain=gChain1))} or {(resno > k) and (chain=gChain2)}) toabTrackIdx(bPp.atomIndex, pt, rotors) var bOP1 = {(resno=@{bPp.resno}) and (chain=gChain2) and (atomName="OP1")} var bOP2 = {(resno=@{bPp.resno}) and (chain=gChain2) and (atomName="OP2")} bOP1.xyz = getTetIdx(bO3.atomIndex, bPp.atomIndex, bO5p.atomIndex, 1.5) bOP2.xyz = getTetIdx(bO5p.atomIndex, bPp.atomIndex, bO3.atomIndex, 1.5) var aOP1 = {(resno=@{aP.resno}) and (chain=gChain1) and (atomName="OP1")} var aOP2 = {(resno=@{aP.resno}) and (chain=gChain1) and (atomName="OP2")} aOP1.xyz = getTetIdx(aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, 1.5) aOP2.xyz = getTetIdx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.5) } bSet = bset or pSet if (k > 0) { k-- } } # endfor } # Bound to ALT-LEFT-CLICK by plicoToabNt function toabChainMB() { color {all} @gScheme gChain1 = {atomIndex=_atomPicked}.chain color {chain=gChain1} @gAltScheme refresh toabNt(FALSE) } # Top level of ToABnt function plicoToabNT() { # Load common functions if not already if (kCommon < 1) { script $SCRIPT_PATH$plicoCommon.spt if (kCommon < 1) { prompt ("A newer version of plicoCommon.SPT is required") quit } } gPlico = "TO A-FORM/B-FORM" plicoPrelim() gEcho = ("________A <==> B_______|ALT-CLICK=mark chain|DOUBLE-CLICK=exit") echo @gEcho gChain = "" unbind bind "ALT-LEFT-CLICK" "_pickAtom"; bind "ALT-LEFT-CLICK" "+:toabChainMB"; bind "DOUBLE" "plicoExit"; } # End of TURN.SPT