User:Remig/plico/plots
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Plots allows the user to generate explorable 3D plots of various interesting aspects of protein folding such as O rotations, chi values, and phi psi values. A menu is presented of available actions:
Plot O rotations - plot the phi and psi angle on either side of all peptide bonds. This is useful to view where O atoms have been pushed aside.
Plot CHIs 1&2 - plot chi values 1 & 2 (0 if n/a).
Plot CHIs 2&3 - plot chi values 2 & 3 (0 if n/a).
Plot PHIs and PSIs - a Ramachandran plot.
Back - exit plots.
All plots have 'resno' as the third dimension. The plots are of the vx and vx values of a single atom from each residue (N or CA). The vx and vy values are overloaded with the values of interest before the plot is generated.
Note that display, select, color, halo on/off, etc. commands may be applied to the plot to highlight and identify areas and aspects of interest.
Plots 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 Plots Script=script <path to your script directory>/plots.spt;plico_plots
saved as Plots.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 plots.spt.
# plots - Jmol script by Ron Mignery
# v1.0 beta 9/11/2015
#
function plot_chis12() {
print "Plotting CHIs 1&2"
select none
var iChain = ""
var chains = {not hoh and not ligands and thisModel}.chain
for (var c = 1; c <= chains.size; c++) {
if (iChain != chains[c]) {
iChain = chains[c]
for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
var aN = get_atom_rcn(i, iChain, "N")
var aCA = get_atom_rcn(i, iChain, "CA")
var aCB = get_atom_rcn(i, iChain, "CB")
var aCG = get_atom_rcn(i, iChain, "?G")
if (aCG.size == 0) {
aCG = get_atom_rcn(i, iChain, "?G1")
}
var aCD = get_atom_rcn(i, iChain, "?D")
if (aCD.size == 0) {
aCD = get_atom_rcn(i, iChain, "?D1")
}
if (aCG) {
aCA.vx = angle(aN, aCA, aCB, aCG)
if (aCD) {
aCA.vy = angle(aCA, aCB, aCG, aCD)
}
else {
aCA.vy = 0
}
}
else {
aCA.vx = 0
}
select ADD aCA
}
}
}
gPlotEcho[1 + _lastFrame[1]] = "vx = chi 1 (0 if none) vy = chi 2 (0 if none)"
plot properties vx vy resno
}
function plot_chis34( ) {
print "Plotting CHIs 3&4"
select none
var iChain = ""
var chains = {not hoh and not ligands and thisModel}.chain
for (var c = 1; c <= chains.size; c++) {
if (iChain != chains[c]) {
iChain = chains[c]
for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
var aCA = get_atom_rcn(i, iChain, "CA")
var aCB = get_atom_rcn(i, iChain, "CB")
var aCG = get_atom_rcn(i, iChain, "?G")
if (aCG.size == 0) {
aCG = get_atom_rcn(i, iChain, "?G1")
}
var aCD = get_atom_rcn(i, iChain, "?D")
if (aCD.size == 0) {
aCD = get_atom_rcn(i, iChain, "?D1")
}
var aCE = get_atom_rcn(i, iChain, "?E")
if (aCE.size == 0) {
aCE = get_atom_rcn(i, iChain, "?E1")
}
var aCZ = get_atom_rcn(i, iChain, "?Z")
if (aCZ.size == 0) {
aCZ = get_atom_rcn(i, iChain, "?Z1")
}
if (aCE) {
aCA.vx = angle(aCB, aCG, aCD, aCE)
if (aCZ) {
aCA.vy = angle(aCG, aCD, aCE, aCZ)
}
else {
aCA.vy = 0
}
}
else {
aCA.vx = 0
}
select ADD aCA
}
}
}
gPlotEcho[1 + _lastFrame[1]] = "vx = chi 3 (0 if none) vy = chi 4 (0 if none)"
plot properties resno vx vy
}
function plot_o_rot() {
print "Plotting O rotations"
select none
var first = true
var aNp = ({})
var aCAp = ({})
var aCp = ({})
var iChain = ""
var chains = {not hoh and not ligands and thisModel}.chain
for (var c = 1; c <= chains.size; c++) {
if (iChain != chains[c]) {
iChain = chains[c]
for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
var aN = get_atom_rcn(i, iChain, "N")
var aCA = get_atom_rcn(i, iChain, "CA")
var aC = get_atom_rcn(i, iChain, "C")
if (first) {
first = false
}
else {
aN.vx = angle(aCp, aN, aCA, aC)
aN.vy = angle(aNp, aCAp, aCp, aN)
select ADD aN
}
aNp = aN
aCAp = aCA
aCp = aC
}
}
}
gPlotEcho[1 + _lastFrame[1]] = "vx = phi vy = n-ward psi"
plot properties vx resno vy
}
function plot_phis_and_psis() {
print "Plotting PHIs and PSIs"
select none
var first = true
var aCp = ({})
var iChain = ""
var chains = {not hoh and not ligands and thisModel}.chain
for (var c = 1; c <= chains.size; c++) {
if (iChain != chains[c]) {
iChain = chains[c]
for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
var aN = get_atom_rcn(i, iChain, "N")
var aCA = get_atom_rcn(i, iChain, "CA")
var aC = get_atom_rcn(i, iChain, "C")
var aNn = get_atom_rcn(i+1, iChain, "N")
if (first) {
first = false
}
else if (aNn) {
aCA.vx = angle(aCp, aN, aCA, aC) #phi
aCA.vy = angle(aN, aCA, aC, aNn) #psi
select ADD aCA
}
aCp = aC
}
}
}
gPlotEcho[1 + _lastFrame[1]] = "vx = phi vy = psi"
plot properties vy resno vx
}
# Callback and plot frames persist if plots closed with just yes
function plot_frame_callback() {
if (_currentFrame > 0) {
unbind "LEFT-CLICK" "+:plico_menu_toggle";
unbind "LEFT-CLICK" "+:plots_click_mb";
set echo top left
color echo red
background echo yellow
echo @{gPlotEcho[1+_currentFrame]}
}
else {
if (gPlico == "PLOTS") {
bind "LEFT-CLICK" "+:plico_menu_toggle";
bind "LEFT-CLICK" "+:plots_click_mb";
}
set echo top left
color echo black
background echo lightgrey
echo @gEcho
}
}
function plots_click_mb() {
# If in menu zone
if ((_mouseX < 100) and ((_height-_mouseY) < 343)) {
var line = ((_mouseX < 125) ? ((_height-_mouseY)\26) : 0)
switch (line) {
case 1:
plot_o_rot()
break
case 2:
plot_chis12()
break
case 3:
plot_chis34()
break
case 4:
plot_phis_and_psis()
break
case 5:
plots_exit()
break
}
}
}
# Top level of plots
function plico_plots() {
# Load common functions if not already
if (kCommon < 6) {
script $SCRIPT_PATH$plicoCommon.spt
if (kCommon < 6) {
prompt ("A newer version of plicoCommon.SPT is required")
quit
}
}
gPlico = "PLOTS"
gPlotEcho = []
plico_prelim(false, true)
gEcho="______Menu_______|Plot O rotations|Plot CHIs 1&2|Plot CHIs 3&4|" +
"Plot PHIs and PSIs| BACK"
set echo top left
color echo black
background echo lightgrey
echo @gEcho
bind "SHIFT-DOUBLE" "plots_exit";
bind "LEFT-CLICK" "+:plico_menu_toggle";
bind "LEFT-CLICK" "+:plots_click_mb";
set AnimFrameCallback "jmolscript:plot_frame_callback"
}
function plots_exit() {
if (plico_exit(true)) {
reset gEcho
display all
gPlico = ""
}
}
# End of PLOTS.SPT
