Difference between revisions of "User:Remig/plico/toab"
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Copy and paste the following into a text editor and save in your scripts directory as toab.spt. | Copy and paste the following into a text editor and save in your scripts directory as toab.spt. | ||
− | <pre># | + | <pre># toAlphaBeta - Jmol script by Ron Mignery |
− | # v1. | + | # v1.7 beta 4/12/2016 -require latest common includes |
# | # | ||
# Move a stretch of polypeptide from alpha to beta or vice versa | # Move a stretch of polypeptide from alpha to beta or vice versa | ||
+ | # or change an amino acid to alpha, beta or L | ||
# | # | ||
gToab = false | gToab = false | ||
Line 52: | Line 53: | ||
function to_ab_drag() { | function to_ab_drag() { | ||
− | |||
− | |||
if (not gBusy) { | if (not gBusy) { | ||
gBusy = true | gBusy = true | ||
Line 96: | Line 95: | ||
m = {atomIndex=_atomPicked}.model | m = {atomIndex=_atomPicked}.model | ||
var nIdx = gNcargoIdx | var nIdx = gNcargoIdx | ||
− | var cmin = {(chain=gChain) and | + | var cmin = {(chain=gChain) and thisModel}.atomno.min |
− | var cmax = {(chain=gChain) and | + | var cmax = {(chain=gChain) and thisModel}.atomno.max |
− | var maxIdx = {(atomno=cmax) and (chain=gchain) and | + | var maxIdx = {(atomno=cmax) and (chain=gchain) and thisModel}.atomIndex |
− | + | var minIdx = {(atomno=cmin) and (chain=gchain) and thisModel}.atomIndex | |
− | var minIdx = {(atomno=cmin) and (chain=gchain) and | ||
− | |||
while (true) { | while (true) { | ||
Line 108: | Line 105: | ||
var caIdx = get_cward_bb_idx(nIdx, gChain) | var caIdx = get_cward_bb_idx(nIdx, gChain) | ||
var cIdx = get_cward_bb_idx(caIdx, gChain) | var cIdx = get_cward_bb_idx(caIdx, gChain) | ||
− | var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx}, | + | if (ncIdx >= 0) { |
− | + | var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx}, | |
− | + | {atomIndex=caIdx}, {atomIndex=cIdx}) | |
− | + | var dir = ((phi > dh) ? abs(8*dx) : -(abs(8*dx))) | |
− | + | if (not gToabAlt) { | |
− | + | select_nward_idx(nIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx)) | |
− | + | } | |
− | + | else { | |
− | + | select_cward_idx(caIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx)) | |
− | + | } | |
− | + | if (abs(phi-dh) > 0.5) { | |
+ | rotate_selected_record(caIdx, {atomIndex=nIdx}, dir) | ||
+ | } | ||
} | } | ||
Line 152: | Line 151: | ||
and not {selected} and not connected({selected})) | and not {selected} and not connected({selected})) | ||
gOk2 = true | gOk2 = true | ||
− | if (lcset | + | if (lcset) { |
for (var i = 1; i <= lcset.size; i++) { | for (var i = 1; i <= lcset.size; i++) { | ||
− | + | to_handle_collisions(lcset[i].atomIndex) | |
} | } | ||
} | } | ||
Line 187: | Line 186: | ||
function to_ab_cargo_mb() { | function to_ab_cargo_mb() { | ||
gToab = true | gToab = true | ||
− | tug_cargo_mb | + | tug_cargo_mb() |
+ | } | ||
+ | |||
+ | function set_phi_psi( r, iChain, phi, psi) { | ||
+ | var aCp = get_atom_rcn( r-1, iChain, "C") | ||
+ | var aN = get_atom_rcn( r, iChain, "N") | ||
+ | var aCA = get_atom_rcn( r, iChain, "CA") | ||
+ | var aC = get_atom_rcn( r, iChain, "C") | ||
+ | var aO = get_atom_rcn( r, iChain, "O") | ||
+ | var aNn = get_atom_rcn( r+1, iChain, "N") | ||
+ | if (aNn) { | ||
+ | select {(resno <= r) and not aC and not aO and chain=iChain | ||
+ | and thisModel} | ||
+ | set_dihedral_atoms(aNn, aC, aCA, aN, psi) | ||
+ | } | ||
+ | if (aCp) { | ||
+ | select {(resno < r) and chain=iChain and thisModel} | ||
+ | set_dihedral_atoms(aC, aCA, aN, aCp, phi) | ||
+ | } | ||
+ | color {resno=r} @gAltScheme | ||
+ | color {(resno=r) and oxygen} pink | ||
+ | } | ||
+ | |||
+ | # Bound to ALT-SHIFT-LEFT-CLICK by plico_to_ab | ||
+ | function to_alpha_mb() { | ||
+ | var r = {atomIndex=_atomPicked}.resno | ||
+ | var iChain = {atomIndex=_atomPicked}.chain | ||
+ | print r+" to alpha" | ||
+ | set_phi_psi( r, iChain, -50, -45) | ||
+ | } | ||
+ | |||
+ | # Bound to CTRL-SHIFT-LEFT-CLICK by plico_to_ab | ||
+ | function to_beta_mb() { | ||
+ | var r = {atomIndex=_atomPicked}.resno | ||
+ | var iChain = {atomIndex=_atomPicked}.chain | ||
+ | print r+" to beta" | ||
+ | set_phi_psi( r, iChain, -100, 135) | ||
+ | } | ||
+ | |||
+ | # Bound to ALT-CTRL-LEFT-CLICK by plico_to_ab | ||
+ | function to_L_mb() { | ||
+ | print "L" | ||
+ | var r = {atomIndex=_atomPicked}.resno | ||
+ | var iChain = {atomIndex=_atomPicked}.chain | ||
+ | set_phi_psi( r, iChain, 50, 45) | ||
+ | } | ||
+ | |||
+ | function to_ab_menu_mb() { | ||
+ | gEcho="______Menu_______|Twist|Bend|SuperCoil| BACK" | ||
+ | set echo top left | ||
+ | color echo black | ||
+ | background echo lightgrey | ||
+ | echo @gEcho | ||
+ | |||
+ | bind "LEFT-CLICK" "+:to_ab_routines_mb"; | ||
+ | } | ||
+ | |||
+ | function to_ab_routines_mb() { | ||
+ | # If in menu zone | ||
+ | if ((_mouseX < 100) and ((_height-_mouseY) < 343)) { | ||
+ | var line = ((_mouseX < 125) ? ((_height-_mouseY)\26) : 0) | ||
+ | switch (line) { | ||
+ | case 1: | ||
+ | print "twistTBD" | ||
+ | break | ||
+ | case 2: | ||
+ | print "bendTBD" | ||
+ | break | ||
+ | case 3: | ||
+ | print "supercoilTBD" | ||
+ | break | ||
+ | case 4: | ||
+ | plico_to_ab() | ||
+ | break | ||
+ | } | ||
+ | } | ||
} | } | ||
Line 194: | Line 268: | ||
# Load common functions if not already | # Load common functions if not already | ||
− | if (kCommon < | + | if (kCommon < 7) { |
script $SCRIPT_PATH$plicoCommon.spt | script $SCRIPT_PATH$plicoCommon.spt | ||
− | if (kCommon < | + | if (kCommon < 7) { |
prompt ("A newer version of plicoCommon.SPT is required") | prompt ("A newer version of plicoCommon.SPT is required") | ||
quit | quit | ||
} | } | ||
} | } | ||
+ | |||
+ | # Load tug functions if not already | ||
if (kTug < 3) { | if (kTug < 3) { | ||
script $SCRIPT_PATH$tug.spt | script $SCRIPT_PATH$tug.spt | ||
if (kTug < 3) { | if (kTug < 3) { | ||
− | prompt ("A newer version of | + | prompt ("A newer version of tug.SPT is required") |
quit | quit | ||
} | } | ||
Line 210: | Line 286: | ||
gPlico = "TO ALPHA/BETA" | gPlico = "TO ALPHA/BETA" | ||
− | plico_prelim(true) | + | plico_prelim(true, true) |
− | gEcho = (" | + | gEcho = ("______Alpha <==> Beta______|ALT-CLICK=mark block" + |
+ | "|CTRL-SHIFT-CLICK=to beta|ALT-SHIFT-CLICK=to alpha" + | ||
+ | "|ALT-CTRL-CLICK=to L|CTRL-CLICK=menu|SHIFT-DOUBLE-CLICK=exit") | ||
echo @gEcho | echo @gEcho | ||
− | |||
− | |||
− | |||
bind "ALT-LEFT-CLICK" "_pickAtom"; | bind "ALT-LEFT-CLICK" "_pickAtom"; | ||
bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; | bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; | ||
− | bind "DOUBLE" "plico_exit"; | + | bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom"; |
+ | bind "ALT-SHIFT-LEFT-CLICK" "+:to_alpha_mb"; | ||
+ | bind "CTRL-SHIFT-LEFT-CLICK" "_pickAtom"; | ||
+ | bind "CTRL-SHIFT-LEFT-CLICK" "+:to_beta_mb"; | ||
+ | bind "ALT-CTRL-LEFT-CLICK" "_pickAtom"; | ||
+ | bind "ALT-CTRL-LEFT-CLICK" "+:to_L_mb"; | ||
+ | bind "CTRL-LEFT-CLICK" "to_ab_menu_mb"; | ||
+ | unbind "CTRL-LEFT-DOWN" | ||
+ | bind "SHIFT-DOUBLE" "plico_exit(true)"; | ||
bind "LEFT-CLICK" "+:plico_menu_toggle"; | bind "LEFT-CLICK" "+:plico_menu_toggle"; | ||
+ | } | ||
+ | |||
+ | # MENU functions | ||
+ | function toab_twist(iChain, rmin, rmax, phi, psi, omega) { | ||
+ | if (rmin < 0) { | ||
+ | rmin = get_resno_min(iChain) | ||
+ | } | ||
+ | if (rmax < 0) { | ||
+ | rmax = get_resno_max(iChain) | ||
+ | } | ||
+ | for (var r = rmin; r <= rmax; r++) { | ||
+ | var aCAp = get_atom_rcn(r-1, iChain, "CA") | ||
+ | var aCp = get_atom_rcn(r-1, iChain, "C") | ||
+ | var aN = get_atom_rcn(r, iChain, "N") | ||
+ | var aCA = get_atom_rcn(r, iChain, "CA") | ||
+ | var aC = get_atom_rcn(r, iChain, "C") | ||
+ | var aO = get_atom_rcn(r, iChain, "O") | ||
+ | var aNn = get_atom_rcn(r+1, iChain, "N") | ||
+ | if (aNn) { | ||
+ | select {(resno > r) or aO} | ||
+ | print "psi=t" | ||
+ | if (x1) throw context t | ||
+ | set_dihedral_atoms(aN, aCA, aC, aNn, psi) | ||
+ | } | ||
+ | if (aCp) { | ||
+ | select {(resno >= r)} | ||
+ | print "phi=t" | ||
+ | if (x1) throw context t | ||
+ | set_dihedral_atoms(aCAp, aCp, aN, aCA, omega) | ||
+ | set_dihedral_atoms(aCp, aN, aCA, aC, phi) | ||
+ | } | ||
+ | } | ||
+ | } | ||
+ | |||
+ | function toab_bend(iChain, rmin, rmax, cacn, cnca, ncac) { | ||
+ | if (rmin < 0) { | ||
+ | rmin = get_resno_min(iChain) | ||
+ | } | ||
+ | if (rmax < 0) { | ||
+ | rmax = get_resno_max(iChain) | ||
+ | } | ||
+ | for (var r = rmin; r <= rmax; r++) { | ||
+ | var aCAp = get_atom_rcn(r-1, iChain, "CA") | ||
+ | var aCp = get_atom_rcn(r-1, iChain, "C") | ||
+ | var aN = get_atom_rcn(r, iChain, "N") | ||
+ | var aCA = get_atom_rcn(r, iChain, "CA") | ||
+ | var aC = get_atom_rcn(r, iChain, "C") | ||
+ | var aO = get_atom_rcn(r, iChain, "O") | ||
+ | var aNn = get_atom_rcn(r+1, iChain, "N") | ||
+ | if (aCp) { | ||
+ | select {(resno >= r) or aOp} | ||
+ | print "phi=t" | ||
+ | if (x1) throw context t | ||
+ | set_angle_atoms(aCAp, aCp, aN, cacn) | ||
+ | select remove aOp | ||
+ | set_angle_atoms(aCp, aN, aCA, cnca) | ||
+ | } | ||
+ | select {(resno > r) or aO or aC} | ||
+ | print "psi=t" | ||
+ | if (x1) throw context t | ||
+ | set_angle_atoms(aN, aCA, aC, ncac) | ||
+ | } | ||
+ | } | ||
+ | |||
+ | function toab_supercoil(iChain, rmin, rmax, n, f) { | ||
+ | var delta = [-1, 0, 1, 2, 1, 0, -1] | ||
+ | if (rmin < 0) { | ||
+ | rmin = get_resno_min(iChain) | ||
+ | } | ||
+ | if (rmax < 0) { | ||
+ | rmax = get_resno_max(iChain) | ||
+ | } | ||
+ | for (var r = rmin; r <= rmax; r++) { | ||
+ | |||
+ | var aN = get_atom_rcn(r, iChain, "N") | ||
+ | var aCA = get_atom_rcn(r, iChain, "CA") | ||
+ | var aC = get_atom_rcn(r, iChain, "C") | ||
+ | var aO = get_atom_rcn(r, iChain, "O") | ||
+ | var aNn = get_atom_rcn(r+1, iChain, "N") | ||
+ | if (aNn) { | ||
+ | select {(resno > r) or aO} | ||
+ | var ca = angle(aN, aCA, aC, aNn) | ||
+ | print ca | ||
+ | set_dihedral_atoms(aN, aCA, aC, aNn, ca+(f*delta[n])) | ||
+ | } | ||
+ | n = 1+((++n)%7) | ||
+ | } | ||
} | } | ||
# End of TOAB.SPT</pre> | # End of TOAB.SPT</pre> |
Latest revision as of 17:07, 12 April 2016
ToAlphaBeta allows the user to mark a section of a polypeptide chain to fold towards an alpha helix configuration or towards a beta strand configuration as described here.
ToAlphaBeta 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 To Alpha/Beta Script=script <path to your scripts directory>/toab.spt;plico_to_ab
saved as plicotoab.macro in your .jmol/macros directory as described in Macro.
A copy of the Plico scripts tug.spt and plicoCommon.spt must be in the same directory as this script.
Copy and paste the following into a text editor and save in your scripts directory as toab.spt.
# toAlphaBeta - Jmol script by Ron Mignery # v1.7 beta 4/12/2016 -require latest common includes # # Move a stretch of polypeptide from alpha to beta or vice versa # or change an amino acid to alpha, beta or L # gToab = false gToabAlt = false gBusy = false # Bound to LEFT-UP by to_ab_enable_drag function to_ab_drag_done_mb() { if (not gToabAlt) { if (gNanchorIdx >= 0) { tug_drag_done_mb() } } else { if (gCanchorIdx >= 0) { tug_drag_done_mb() } } } # Bound to ALT-SHIFT-LEFT-DRAG by to_ab_enable_drag function to_ab_drag_2_mb() { gToabAlt = true to_ab_drag() } # Bound to ALT-LEFT-DRAG by to_ab_enable_drag function to_ab_drag_mb() { gToabAlt = false to_ab_drag() } # Bound to ALT-LEFT-DOWN by tug_enable_drag function tug_mark_mb() { gMouseX = _mouseX gMouseY = _mouseY gNewDrag = true } function to_ab_drag() { if (not gBusy) { gBusy = true var dx = (40.0 * (_mouseX - gMouseX))/_width var dy = (40.0 * (_mouseY - gMouseY))/_height var q = quaternion() var ptd = {@dx @dy 0} var pt = (!q)%ptd if (distance(pt, {0 0 0}) > 0.004) { # If sidechain mode if (gSCidx >= 0) { if ({atomIndex=gSCidx}.atomName == "O") { var dir = ((abs(dx) > abs(dy)) ? ((dx < 0) ? 2 : -2) : ((dy < 0) ? 2 : -2)) counterRotate(gSCidx, dir, not gToabAlt) } else { gSCcheck = not gToabAlt tugSideChain(pt) } } # Else else { # If new drag if (gNewDrag) { gNewDrag = false save state gState } # Move the cargo select {gCargoSet} var phi = ((dx < 0) ? -57 : -90) var psi = ((dx < 0) ? -47 : 120) # Move between alpha and beta f = {atomIndex=_atomPicked}.file m = {atomIndex=_atomPicked}.model var nIdx = gNcargoIdx var cmin = {(chain=gChain) and thisModel}.atomno.min var cmax = {(chain=gChain) and thisModel}.atomno.max var maxIdx = {(atomno=cmax) and (chain=gchain) and thisModel}.atomIndex var minIdx = {(atomno=cmin) and (chain=gchain) and thisModel}.atomIndex while (true) { # Adjust phi var ncIdx = get_nward_bb_idx(nIdx, gChain) var caIdx = get_cward_bb_idx(nIdx, gChain) var cIdx = get_cward_bb_idx(caIdx, gChain) if (ncIdx >= 0) { var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx}, {atomIndex=caIdx}, {atomIndex=cIdx}) var dir = ((phi > dh) ? abs(8*dx) : -(abs(8*dx))) if (not gToabAlt) { select_nward_idx(nIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx)) } else { select_cward_idx(caIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx)) } if (abs(phi-dh) > 0.5) { rotate_selected_record(caIdx, {atomIndex=nIdx}, dir) } } # Adjust psi var cnIdx = get_cward_bb_idx (cIdx, gChain) dh= angle({atomIndex=nIdx}, {atomIndex=caIdx}, {atomIndex=cIdx}, {atomIndex=cnIdx}) dir = ((psi > dh) ? abs(8*dx) : -(abs(8*dx))) if (not gToabAlt) { select_nward_idx(caIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx)) } else { select_cward_idx(cIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx)) } if (abs(psi-dh) > 0.5) { rotate_selected_record(cIdx, {atomIndex=caIdx}, dir) } if (gCcargoIdx== cIdx) { break } nIdx = cnIdx } # endwhile } gMouseX = _mouseX gMouseY = _mouseY } select {gCargoSet} var lcset = (within(kCtolerance, false, {selected}) and not {selected} and not connected({selected})) gOk2 = true if (lcset) { for (var i = 1; i <= lcset.size; i++) { to_handle_collisions(lcset[i].atomIndex) } } var bkc = (gOk2 ? "yellow" : "pink") background ECHO @bkc gBusy = false } } # Called by to_ab_cargo_mb when gToab is true function to_ab_enable_drag() { gEcho = "____Alpha <==> Beta____|ALT-CLICK=mark block|SHIFT-CLICK=anchors" + "|ALT-DRAG=move|SHIFT-ALT-DRAG=alt move|DOUBLE-CLICK=exit" echo @gEcho # Allow atoms to be dragged bind "ALT-LEFT-DOWN" "tug_mark_mb"; bind "ALT-LEFT-UP" "tug_drag_done_mb"; bind "ALT-LEFT-DRAG" "to_ab_drag_mb"; bind "ALT-SHIFT-LEFT-UP" "to_ab_drag_done_mb"; bind "ALT-SHIFT-LEFT-DRAG" "to_ab_drag_2_mb"; unbind "SHIFT-LEFT-CLICK" bind "SHIFT-LEFT-CLICK" "_pickAtom"; bind "SHIFT-LEFT-CLICK" "+:tug_anchor_mb"; } # Bound to ALT-LEFT-CLICK by plico_to_ab function to_ab_cargo_mb() { gToab = true tug_cargo_mb() } function set_phi_psi( r, iChain, phi, psi) { var aCp = get_atom_rcn( r-1, iChain, "C") var aN = get_atom_rcn( r, iChain, "N") var aCA = get_atom_rcn( r, iChain, "CA") var aC = get_atom_rcn( r, iChain, "C") var aO = get_atom_rcn( r, iChain, "O") var aNn = get_atom_rcn( r+1, iChain, "N") if (aNn) { select {(resno <= r) and not aC and not aO and chain=iChain and thisModel} set_dihedral_atoms(aNn, aC, aCA, aN, psi) } if (aCp) { select {(resno < r) and chain=iChain and thisModel} set_dihedral_atoms(aC, aCA, aN, aCp, phi) } color {resno=r} @gAltScheme color {(resno=r) and oxygen} pink } # Bound to ALT-SHIFT-LEFT-CLICK by plico_to_ab function to_alpha_mb() { var r = {atomIndex=_atomPicked}.resno var iChain = {atomIndex=_atomPicked}.chain print r+" to alpha" set_phi_psi( r, iChain, -50, -45) } # Bound to CTRL-SHIFT-LEFT-CLICK by plico_to_ab function to_beta_mb() { var r = {atomIndex=_atomPicked}.resno var iChain = {atomIndex=_atomPicked}.chain print r+" to beta" set_phi_psi( r, iChain, -100, 135) } # Bound to ALT-CTRL-LEFT-CLICK by plico_to_ab function to_L_mb() { print "L" var r = {atomIndex=_atomPicked}.resno var iChain = {atomIndex=_atomPicked}.chain set_phi_psi( r, iChain, 50, 45) } function to_ab_menu_mb() { gEcho="______Menu_______|Twist|Bend|SuperCoil| BACK" set echo top left color echo black background echo lightgrey echo @gEcho bind "LEFT-CLICK" "+:to_ab_routines_mb"; } function to_ab_routines_mb() { # If in menu zone if ((_mouseX < 100) and ((_height-_mouseY) < 343)) { var line = ((_mouseX < 125) ? ((_height-_mouseY)\26) : 0) switch (line) { case 1: print "twistTBD" break case 2: print "bendTBD" break case 3: print "supercoilTBD" break case 4: plico_to_ab() break } } } # Top level of ToAlphaBeta function plico_to_ab() { # Load common functions if not already if (kCommon < 7) { script $SCRIPT_PATH$plicoCommon.spt if (kCommon < 7) { prompt ("A newer version of plicoCommon.SPT is required") quit } } # Load tug functions if not already if (kTug < 3) { script $SCRIPT_PATH$tug.spt if (kTug < 3) { prompt ("A newer version of tug.SPT is required") quit } } gPlico = "TO ALPHA/BETA" plico_prelim(true, true) gEcho = ("______Alpha <==> Beta______|ALT-CLICK=mark block" + "|CTRL-SHIFT-CLICK=to beta|ALT-SHIFT-CLICK=to alpha" + "|ALT-CTRL-CLICK=to L|CTRL-CLICK=menu|SHIFT-DOUBLE-CLICK=exit") echo @gEcho bind "ALT-LEFT-CLICK" "_pickAtom"; bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom"; bind "ALT-SHIFT-LEFT-CLICK" "+:to_alpha_mb"; bind "CTRL-SHIFT-LEFT-CLICK" "_pickAtom"; bind "CTRL-SHIFT-LEFT-CLICK" "+:to_beta_mb"; bind "ALT-CTRL-LEFT-CLICK" "_pickAtom"; bind "ALT-CTRL-LEFT-CLICK" "+:to_L_mb"; bind "CTRL-LEFT-CLICK" "to_ab_menu_mb"; unbind "CTRL-LEFT-DOWN" bind "SHIFT-DOUBLE" "plico_exit(true)"; bind "LEFT-CLICK" "+:plico_menu_toggle"; } # MENU functions function toab_twist(iChain, rmin, rmax, phi, psi, omega) { if (rmin < 0) { rmin = get_resno_min(iChain) } if (rmax < 0) { rmax = get_resno_max(iChain) } for (var r = rmin; r <= rmax; r++) { var aCAp = get_atom_rcn(r-1, iChain, "CA") var aCp = get_atom_rcn(r-1, iChain, "C") var aN = get_atom_rcn(r, iChain, "N") var aCA = get_atom_rcn(r, iChain, "CA") var aC = get_atom_rcn(r, iChain, "C") var aO = get_atom_rcn(r, iChain, "O") var aNn = get_atom_rcn(r+1, iChain, "N") if (aNn) { select {(resno > r) or aO} print "psi=t" if (x1) throw context t set_dihedral_atoms(aN, aCA, aC, aNn, psi) } if (aCp) { select {(resno >= r)} print "phi=t" if (x1) throw context t set_dihedral_atoms(aCAp, aCp, aN, aCA, omega) set_dihedral_atoms(aCp, aN, aCA, aC, phi) } } } function toab_bend(iChain, rmin, rmax, cacn, cnca, ncac) { if (rmin < 0) { rmin = get_resno_min(iChain) } if (rmax < 0) { rmax = get_resno_max(iChain) } for (var r = rmin; r <= rmax; r++) { var aCAp = get_atom_rcn(r-1, iChain, "CA") var aCp = get_atom_rcn(r-1, iChain, "C") var aN = get_atom_rcn(r, iChain, "N") var aCA = get_atom_rcn(r, iChain, "CA") var aC = get_atom_rcn(r, iChain, "C") var aO = get_atom_rcn(r, iChain, "O") var aNn = get_atom_rcn(r+1, iChain, "N") if (aCp) { select {(resno >= r) or aOp} print "phi=t" if (x1) throw context t set_angle_atoms(aCAp, aCp, aN, cacn) select remove aOp set_angle_atoms(aCp, aN, aCA, cnca) } select {(resno > r) or aO or aC} print "psi=t" if (x1) throw context t set_angle_atoms(aN, aCA, aC, ncac) } } function toab_supercoil(iChain, rmin, rmax, n, f) { var delta = [-1, 0, 1, 2, 1, 0, -1] if (rmin < 0) { rmin = get_resno_min(iChain) } if (rmax < 0) { rmax = get_resno_max(iChain) } for (var r = rmin; r <= rmax; r++) { var aN = get_atom_rcn(r, iChain, "N") var aCA = get_atom_rcn(r, iChain, "CA") var aC = get_atom_rcn(r, iChain, "C") var aO = get_atom_rcn(r, iChain, "O") var aNn = get_atom_rcn(r+1, iChain, "N") if (aNn) { select {(resno > r) or aO} var ca = angle(aN, aCA, aC, aNn) print ca set_dihedral_atoms(aN, aCA, aC, aNn, ca+(f*delta[n])) } n = 1+((++n)%7) } } # End of TOAB.SPT