Remig at 17:38, 12 April 2016

2016-04-12T17:38:08Z

Remig: Some useful plots for manually folding polyopeptides

2015-09-11T16:23:42Z

Some useful plots for manually folding polyopeptides

New page

'''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 [[User:Remig/plico|here]]. It may be installed and accessed as a macro with the file:
<pre>Title=PLICO Plots
Script=script <path to your script directory>/plots.spt;plico_plots
</pre>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.

<pre># 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
</pre>

@@ Line 23: / Line 23: @@
 <pre>#   plots - Jmol script by Ron Mignery
-#   v1.0 beta    9/11/2015
+#   v1.1 beta    4/12/2016 -require latest common includes
+#
@@ Line 30: / Line 30: @@
      select none
      var iChain = ""
      var chains = {not hoh and not ligands and thisModel}.chain
@@ Line 36: / Line 37: @@
              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")
@@ Line 61: / Line 63: @@
                  select ADD aCA
+             }
+         }
+     }
-     gPlotEcho[1 + _lastFrame[1]] = "vx = chi 1 (0 if none)        vy = chi 2 (0 if none)"
+     gPlotEcho[1 + _lastFrame[1]] = "vx = chi 1 (0 if none)        vy = chi 2 (0 if none)  {hover = chi1 chi2 resno)"
-     plot properties vx vy resno
+     plot properties vx vy resno MIN{-180, -180, 1} MAX{180, 180, @resmax}
+}
@@ Line 71: / Line 80: @@
      print "Plotting CHIs 3&4"
      select none
      var iChain = ""
      var chains = {not hoh and not ligands and thisModel}.chain
@@ Line 95: / Line 105: @@
                      aCZ = get_atom_rcn(i, iChain, "?Z1")
+                 }
-                 if (aCE) {
+                 if (aCE.size > 0) {
                      aCA.vx = angle(aCB, aCG, aCD, aCE)
-                     if (aCZ) {
+                     if (aCZ.size > 0) {
                          aCA.vy = angle(aCG, aCD, aCE, aCZ)
+                     }
@@ Line 109: / Line 119: @@
                  select ADD aCA
+             }
+         }
+     }
-     gPlotEcho[1 + _lastFrame[1]] = "vx = chi 3 (0 if none)        vy = chi 4 (0 if none)"
+     gPlotEcho[1 + _lastFrame[1]] = "vx = chi 3 (0 if none)        vy = chi 4 (0 if none)  {hover = resno chi3 chi4)"
-     plot properties resno vx vy
+     plot properties resno vx vy MIN{1, -180, -180} MAX{@resmax, 180, 180}
+}
@@ Line 123: / Line 136: @@
      var aCAp = ({})
      var aCp = ({})
      var iChain = ""
      var chains = {not hoh and not ligands and thisModel}.chain
@@ Line 144: / Line 158: @@
                  aCAp = aCA
                  aCp = aC
+             }
+         }
+     }
-     gPlotEcho[1 + _lastFrame[1]] = "vx = phi        vy = n-ward psi"
+     gPlotEcho[1 + _lastFrame[1]] = "vx = phi        vy = n-ward psi  (hover = phi resno psi)"
-     plot properties vx resno vy
+     plot properties vx resno vy MIN{-180, 1, -180} MAX{180, @resmax, 180}
+}
@@ Line 156: / Line 173: @@
      var first = true
      var aCp = ({})
      var iChain = ""
      var chains = {not hoh and not ligands and thisModel}.chain
@@ Line 176: / Line 194: @@
+                 }
                  aCp = aC
+             }
+         }
+     }
-     gPlotEcho[1 + _lastFrame[1]] = "vx = phi        vy = psi"
+     gPlotEcho[1 + _lastFrame[1]] = "vx = phi        vy = psi   (hover = psi resno phi)"
-     plot properties vy resno vx
+     plot properties vy resno vx MIN{-180, 1, -180} MAX{180, @resmax, 180}
+}
@@ Line 234: / Line 255: @@
      # Load common functions if not already
-     if (kCommon < 6) {
+     if (kCommon < 7) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 6) {
+         if (kCommon < 7) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit

User:Remig/plico/plots - Revision history

Remig at 17:38, 12 April 2016

Remig: Some useful plots for manually folding polyopeptides