Difference between revisions of "User:Remig/plico/toab"
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(Handle multi-frame environment) |
(Add toggle menu) |
||
Line 9: | Line 9: | ||
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># toAB - Jmol script by Ron Mignery |
− | # v1. | + | # v1.4 beta 7/24/2015 -add menu toggle |
# | # | ||
# Move a stretch of polypeptide from alpha to beta or vice versa | # Move a stretch of polypeptide from alpha to beta or vice versa | ||
Line 66: | Line 66: | ||
if (gSCidx >= 0) { | if (gSCidx >= 0) { | ||
if ({atomIndex=gSCidx}.atomName == "O") { | if ({atomIndex=gSCidx}.atomName == "O") { | ||
− | dir = ((abs(dx) > abs(dy)) | + | var dir = ((abs(dx) > abs(dy)) |
? ((dx < 0) ? 2 : -2) | ? ((dx < 0) ? 2 : -2) | ||
: ((dy < 0) ? 2 : -2)) | : ((dy < 0) ? 2 : -2)) | ||
Line 154: | Line 154: | ||
if (lcset.size > 0) { | if (lcset.size > 0) { | ||
for (var i = 1; i <= lcset.size; i++) { | for (var i = 1; i <= lcset.size; i++) { | ||
− | + | handle_collisions(lcset[i].atomIndex) | |
} | } | ||
} | } | ||
Line 186: | Line 186: | ||
# Bound to ALT-LEFT-CLICK by plico_to_ab | # Bound to ALT-LEFT-CLICK by plico_to_ab | ||
function to_ab_cargo_mb() { | function to_ab_cargo_mb() { | ||
− | |||
gToab = true | gToab = true | ||
tug_cargo_mb | tug_cargo_mb | ||
Line 195: | Line 194: | ||
# Load common functions if not already | # Load common functions if not already | ||
− | if (kCommon < | + | if (kCommon < 6) { |
script $SCRIPT_PATH$plicoCommon.spt | script $SCRIPT_PATH$plicoCommon.spt | ||
− | if (kCommon < | + | if (kCommon < 6) { |
prompt ("A newer version of plicoCommon.SPT is required") | prompt ("A newer version of plicoCommon.SPT is required") | ||
quit | quit | ||
Line 216: | Line 215: | ||
echo @gEcho | echo @gEcho | ||
gChain = "" | gChain = "" | ||
+ | gMenuMin = false | ||
unbind | unbind | ||
Line 221: | Line 221: | ||
bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; | bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; | ||
bind "DOUBLE" "plico_exit"; | bind "DOUBLE" "plico_exit"; | ||
+ | bind "LEFT-CLICK" "+:plico_menu_toggle"; | ||
} | } | ||
# End of TOAB.SPT</pre> | # End of TOAB.SPT</pre> |
Revision as of 18:48, 24 July 2015
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.
# toAB - Jmol script by Ron Mignery # v1.4 beta 7/24/2015 -add menu toggle # # Move a stretch of polypeptide from alpha to beta or vice versa # 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() { var f = (_frameID/1000000) var m = (_frameID%1000000) 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 (file=f) and (model=m)}.atomno.min var cmax = {(chain=gChain) and (file=f) and (model=m)}.atomno.max var maxIdx = {(atomno=cmax) and (chain=gchain) and (file=f) and (model=m)}.atomIndex var minIdx = {(atomno=cmin) and (chain=gchain) and (file=f) and (model=m)}.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) 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.size > 0) { for (var i = 1; i <= lcset.size; i++) { 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 } # Top level of ToAlphaBeta function plico_to_ab() { # 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 } } 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) gEcho = ("____Alpha <==> Beta____|ALT-CLICK=mark block|DOUBLE-CLICK=exit") echo @gEcho gChain = "" gMenuMin = false unbind bind "ALT-LEFT-CLICK" "_pickAtom"; bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb"; bind "DOUBLE" "plico_exit"; bind "LEFT-CLICK" "+:plico_menu_toggle"; } # End of TOAB.SPT