User:Remig/plico/toABnt
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ToABnt allows the user to convert a polynucleotide chain or chain pair 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 directory>/toABnt.spt;plico_to_ab_nt
saved as toABnt.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 toABnt.spt.
# toABnt - Jmol script by Ron Mignery
# v1.4 beta 5/16/2014 -lc all functions
#
# Convert a polynucleotide chain from A-form to B-form or vice versa
#
kC5O5PO3B = -71.0
kO5PO3C3B = -106.0
kPO3C3C4B = -160.67
kO3C3C4C5B = 125.44
kC3C4C5O5B = 55.65
kC4C5O5PB = 169.0
kO4C4C3C2B = 15.92
kC4O4C1C2B = -41.7
kC4O4C1NxB = -159.03
kC5C4O4C1B = 146.31
kC3C1C2O2B = -167.9
kPuB = 59.0
kPyB = 61.0
kC5O5PO3A = -59.3
kO5PO3C3A = -63.1
kPO3C3C4A = -157.4
kO3C3C4C5A = 75.5
kC3C4C5O5A = 49.55
kC4C5O5PA = 169.2
kO4C4C3C2A = -35.55
kC4O4C1C2A = 3.8
kC4O4C1NxA = -117.4
kC5C4O4C1A = 144.85
kC3C1C2O2A = 116.3
kPuA = 13.5
kPyA = 16.5
gToab = FALSE
gToabAlt = FALSE
gToA = FALSE
function to_ab_nt_auto(iChain, toA) {
# Load common functions if not already
load_common()
gChain1 = iChain
gToA = toA
to_ab_nt(TRUE)
}
function to_ab_nt(auto) {
if (not gBusy) {
gBusy = TRUE
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 kmax = k
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) {
var isForm = (is_form_a( i, gChain1) ? "A" : "B")
var 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
}
background ECHO pink
refresh
print format("Converting to %s", p)
}
# If paired
var 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)
kmax = k
}
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)}
set_dihedral_atoms(aP, aO3p, aC3p, aC4p, (gToA ? kPO3C3C4A : kPO3C3C4B))
set_dihedral_atoms(aO5, aP, aO3p, aC3p, (gToA ? kO5PO3C3A : kO5PO3C3B))
select bSet or {(atomno < @{aO5.atomno}) and
(atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
set_dihedral_atoms(aC5, aO5, aP, aO3p, (gToA ? kC5O5PO3A : kC5O5PO3B))
}
select bSet or {(atomno < @{aO5.atomno}) and
(atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
set_dihedral_atoms(aC4, aC5, aO5, aP, (gToA ? kC4C5O5PA : kC4C5O5PB))
select (bP or (connected(bP) and {resno=k}))
set_dihedral_atoms(bC4, bC5, bO5, bP, (gToA ? kC4C5O5PA : kC4C5O5PB))
select bSet or {(atomno < @{aC5.atomno}) and
(atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
set_dihedral_atoms(aC3, aC4, aC5, aO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B))
select (bP or (connected(bP) and {resno=k}))
set_dihedral_atoms(bC3, bC4, bC5, bO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B))
select (({(resno >= k) and (chain=gChain2)}
or {(resno <= i) and (chain=gChain1)}) and not aO3)
set_dihedral_atoms(aO3, aC3, aC4, aC5, (gToA ? kO3C3C4C5A : kO3C3C4C5B))
select bO3
set_dihedral_atoms(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}
set_dihedral_atoms(aO4, aC1, aNx, aCx, ang)
select {pSet and not base}
set_dihedral_atoms(bCx, bNx, bC1, bO4, pang)
# Set pucker 3' endo or 2' endo
select pSet or {(resno=i) and (chain=gChain1) and base}
set_dihedral_atoms(aC4, aO4, aC1, aNx, (gToA ? kC4O4C1NxA : kC4O4C1NxB))
select {pSet and not base}
set_dihedral_atoms(bNx, bC1, bO4, bC4, (gToA ? kC4O4C1NxA : kC4O4C1NxB))
select (pSet or
{((resno=i) and (chain=gChain1) and base) or aC1})
set_dihedral_atoms(aC5, aC4, aO4, aC1, (gToA ? kC5C4O4C1A : kC5C4O4C1B))
select {pSet and not base and not bC1}
set_dihedral_atoms(bC1, bO4, bC4, bC5, (gToA ? kC5C4O4C1A : kC5C4O4C1B))
select aC2 or aO2
set_dihedral_atoms(aC4, aO4, aC1, aC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B))
if (aO2.size > 0) {
ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B)
set_dihedral_atoms(aC3, aC1, aC2, aO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B))
}
set_distance_atoms(aC3, aC2, 1.52)
set_distance_atoms(aC1, aC2, 1.52)
select bC2 or bO2
set_dihedral_atoms(bC4, bO4, bC1, bC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B))
if (bO2.size > 0) {
ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B)
set_dihedral_atoms(bC3, bC1, bC2, bO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B))
}
set_distance_atoms(bC3, bC2, 1.52)
set_distance_atoms(bC1, bC2, 1.52)
refresh
bSet = bset or pSet
if (k > 0) {
k--
}
} # endfor
gBusy = FALSE
background ECHO yellow
refresh
}
}
# Bound to ALT-LEFT-CLICK by plicoto_ab_nt
function to_ab_chain_mb() {
color {all} @gScheme
gChain1 = {atomIndex=_atomPicked}.chain
color {chain=gChain1} @gAltScheme
refresh
to_ab_nt(FALSE)
}
# Load common functions if not already
function load_common() {
if (kCommon < 2) {
script $SCRIPT_PATH$plicoCommon.spt
if (kCommon < 2) {
prompt ("A newer version of plicoCommon.SPT is required")
quit
}
}
if (kNTcommon < 2) {
script $SCRIPT_PATH$plicoNTcommon.spt
if (kNTcommon < 2) {
prompt ("A newer version of plicoNTcommon.SPT is required")
quit
}
}
}
# Top level of to_ab_nt
function plico_to_ab_nt() {
# Load common functions if not already
load_common()
gPlico = "TO A-FORM/B-FORM"
plico_prelim(FALSE)
gEcho = ("________A <==> B_______|ALT-CLICK=mark chain|DOUBLE-CLICK=exit")
echo @gEcho
gChain = ""
unbind
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:to_ab_chain_mb";
bind "DOUBLE" "plico_exit";
}
# End of to_ab_nt.SPT
