Remig at 17:33, 12 April 2016

2016-04-12T17:33:30Z

Remig: Add, remove and view polypeptide waters

2015-09-11T15:46:20Z

Add, remove and view polypeptide waters

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Hydrate.spt allows the user to add, remove and view water molecules at appropriate places by clicking on a chain. When viewing water, a menu is presented for selecting among waters hbonded to a single oxygen, two oxygens, three oxygens, a single nitrogen, two nitrogens, three nitrogens, an oxygen and a nitrogen, an oxygen and two nitrogens, two oxygens and one nitrogen, or more than three atoms and atoms with two waters.

Hydrate 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 Hydrate
Script=script <path to your script directory>/hydrate.spt;plico_hydrate
</pre>saved as hydrate.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 hydrate.spt.

<pre># hydrate - Jmol script by Ron Mignery
# v1.0 beta 9/11/2015
#
# View waters of hydration (HOH) iteratively of any model
# or add or delete waters on all available sites
#
# Addition requires space where h-bonding is possible at a distance
# of 2.3 angstrom at an angle > 100 degrees
#
gI = 1
gSel = ""
function add_water(idx) {
f = _frameID/1000000
m = _frameID%1000000
var iChain = {atomIndex=idx}.chain
var ap = {atomIndex=idx}
var pt = {0 0 0}
var cSet = connected(ap)
var tri = false
if (cSet.size == 1) {
var v = ap.xyz - cSet[1].xyz
pt = ap.xyz + v + v
}
else {
pt = get_trigonal_idx(cSet[1].atomIndex, idx, cSet[2].atomIndex, 2.3)
tri = true
}

if (within(kCtolerance, pt).size == 0) {
print "Hydrating " + ap
var ls = "data \"append addto\"\n"
ls += format("ATOM %5d O HOH %s%4d ",
{thisModel}.atomno.max + 1, iChain, ap.resno)
ls += format("%8.3f%8.3f%8.3f\n", pt.x, pt.y, pt.z)
ls += "end \"append addto\""
gAppendNew = appendNew
appendNew = false
script inline @{ls}
appendNew = gAppendNew

var ahoh = {(group="HOH") and within(2.9, ap)}
select @ahoh
color pink
set_distance_atoms(ap, ahoh, 2.3)

if (tri = false) {
var hidx = ahoh.atomIndex
var ccSet = connected(cSet[1])
set_angle_idx(cSet[1].atomIndex, idx, hidx, 120)
set_dihedral_idx(ccSet[1].atomIndex, cSet[1].atomIndex, idx, hidx, 180)
var xset = within(kCtolerance, ahoh) and not ahoh
if ( xset) {
set_dihedral_idx(ccSet[1].atomIndex, cSet[1].atomIndex, idx, hidx, 0)
}
}

var i = 0
for (; i < 360; i += 5) {
var xset = within(kCtolerance, ahoh) and not ahoh
if (xset.size == 0) {
break
}
else if ((xset.size == 1) and (xset[1].group == "HOH")) {
print "share it TBD"
i = 360
break
}
else if (tri) {
i = 360
break
}
rotateSelected @{cset[1]} @ap 5
} # endfor

if ( i >= 360) {
print "no room for water"
delete ahoh
}
}
}

function view_hoh_mb() {
display all
font echo 20
var hset = {hoh}
color @hset pink
o1n0 = []
o0n1 = []
o2n0 = []
o0n2 = []
o1n1 = []
o2n1 = []
o1n2 = []
o3n0 = []
o0n3 = []
xgt3 = []
wxw = []

for (var i = 1; i <= hset.size; i++) {
var ah = hset[i]
var onset = {within(2.9, ah) and (oxygen or nitrogen) and not hoh}
var oc = 0
var nc = 0
for (var j = 1; j <= onset.size; j++) {
var cset = connected(onset[j])
var ok = false
if (cset) {
ok = (angle(cset[1], onset[j], ah) > 100)
}
if ((ok == false) and (cset.size > 1)) {
ok = (angle(cset[2], onset[j], ah) > 100)
}
if (ok) {
if (onset[j].atomName[1]="O") {
oc++
}
else {
nc++
}
}
wxwset = hset and within(2.9, onset[j])
if (wxwset.size > 1) {
wxw = wxw + onset[j]
}
}
var oxnx = (((oc+nc) > 3) ? "xgt3" : format("o%dn%d", oc, nc))
@oxnx = @oxnx + ah
}
#print "=t"
#throw context t
var p1=format("O___[%2d]|OO__[%2d]|OOO_[%2d]|", o1n0.size, o2n0.size, o3n0.size)
var p2=format("___N[%2d]|__NN[%2d]|_NNN[%2d]|", o0n1.size, o0n2.size, o0n3.size)
var p3=fOrmat("O__N[%2d]|O_NN[%2d]|OO_N[%2d]|XGT3[%2d]|WXW [%2d]|",
o1n1.size, o1n2.size, o2n1.size, xgt3.size, wxw.size)
gEcho="__Menu__|"+p1+p2+p3+"QUIT VIEW"
set echo top left
color echo black
background echo lightgrey
echo @gEcho
unbind "ALT-LEFT-CLICK" "+:hydrate_mb";
unbind "ALT-SHIFT-LEFT-CLICK" "+:dehydrate_mb";
#bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "CTRL-LEFT-CLICK" "+:tour_ctrl_click_mb";
bind "LEFT-CLICK" "+:tour_click_mb"

}

function hoh_tour() {
print format("x=%d y=%d", _mouseX, _mouseY)
if ((_mouseX < 100) and ((_height-_mouseY) < 343)) {
var line = ((_mouseX < 125) ? ((_height-_mouseY)\26) : 0)
print format("line=%d", line)
if (gEcho.size > 80) {
if (line ==12) {
select all
halo off
display all
unbind all
background echo yellow
color echo red
measure off
plico_hydrate()
return
}
else if (line < 1) {
return
}
gI = 1
sel = ["o1n0", "o2n0", "o3n0", "o0n1", "o0n2", "o0n3", "o1n1",
"o1n2", "o2n1", "xgt3", "wxw"]
gSel = sel[line]
line = 0
}

var mx = format("%d of %d", gI, @gSel.size)
gEcho = "__Menu__|<= prev | next => | back| " + mx
echo @gEcho

if (line == 1) {
gI--
}

else if (line == 2) {
gI++
}

else if (line == 3) {
view_hoh_mb()
return
}

if (@gSel) {
if (gI < 1) {
gI = @gSel.size
}
if (gi > @gSel.size) {
gi = 1
}
display_around_atom(@gSel[gI])
}
else {
view_hoh_mb()
}
}
}

function display_around_atom(aa) {
halo off
center @aa
var cset = connected(aa)
var ccset = connected(cset) and not aa
var nset = {(within( 2.9, aa) and (oxygen or nitrogen)
and not ccset and not aa) or cset}

select nset or aa
halo on
display within( 6, aa)
measure off
var j = 1
for (var i = 1; i <= nset.size; i++) {
if ((nset[i] and cset).size == 0) {
measure @aa @{nset[i]}
}

if (ccset.size == 0) {
var aset = connected(nset[i])
for (var j = 1; j <= nset.size; j++) {
measure @aa @{nset[i]} @{aset[j]}
}
}
}

if (nset.size > 1) {
measure @{nset[1]} @aa @{nset[2]}
}
if (nset.size > 2) {
measure @{nset[1]} @aa @{nset[3]}
measure @{nset[2]} @aa @{nset[3]}
}
if (nset.size > 2) {
measure @{nset[4]} @aa @{nset[1]}
measure @{nset[4]} @aa @{nset[2]}
measure @{nset[4]} @aa @{nset[3]}
}
print "if x1=t"
if (x1) throw context t
refresh
}

function tour_ctrl_click_mb() {
print _atomPicked
var r = {atomIndex=_atomPicked}.resno
var c = {atomIndex=_atomPicked}.chain
var n = {atomIndex=_atomPicked}.atomName
display add {(resno=r) and (chain=c)}
if (n == "N") {
r--
display add {(resno=r) and (chain=c)}
}
else if (n == "C") {
r++
display add {(resno=r) and (chain=c)}
}
else if (n == "O") {
r++
display add {(resno=r) and (chain=c)}
}
}

function tour_click_mb() {

# If in menu zone
if ((_mouseX < 100) and ((_height-_mouseY) < 343)) {
hoh_tour()
}
else if (_atomPicked >= 0) {

var g = {atomIndex=_atomPicked}.group
var n = {atomIndex=_atomPicked}.atomName
if ((g == "HOH") or (n == "N") or (n =="O")) {
display_around_atom({atomIndex=_atomPicked})
}
}
}

function hydrate_mb() {
iChain = {atomIndex=_atomPicked}.chain
for (var r = get_resno_min(iChain); r <= get_resno_max(iChain); r++) {
var aO = get_atom_rcn( r, iChain, "O")
if (aO.group != "HOH") {
add_water(aO.atomIndex)
}
var aN = get_atom_rcn( r, iChain, "N")
add_water(aN.atomIndex)
}
}

function dehydrate_mb() {
iChain = {atomIndex=_atomPicked}.chain
delete {hoh and (chain=iChain) and thisModel}
}

# Top level of hydrate
function plico_hydrate() {

# 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 = "HYDRATE"
plico_prelim(false, true)

gEcho = ("________HYDRATE________|ALT-CLICK=hydrate chain|" +
"ALT-SHIFT-CLICK=dehydrate chain|" +
"CTRL-CLICK=view HOHs|SHIFT-DOUBLE-CLICK=exit")
echo @gEcho

bind "ALT-LEFT-CLICK" "_pickAtom"
bind "ALT-LEFT-CLICK" "+:hydrate_mb"
bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom"
bind "ALT-SHIFT-LEFT-CLICK" "+:dehydrate_mb"
unbind "CTRL-LEFT-DOWN"
bind "CTRL-LEFT-CLICK" "view_hoh_mb"
bind "SHIFT-DOUBLE" "hydrate_exit"
bind "LEFT-CLICK" "+:plico_menu_toggle"

}

function hydrate_exit() {
if (plico_exit(true)) {
reset gI
reset gSel
reset o1n0
reset o0n1
reset o2n0
reset o0n2
reset o1n1
reset o2n1
reset o1n2
reset o3n0
reset o0n3
reset xgt3
reset wxw
display all
}
}
# End of HYDRATE.SPT
</pre>

@@ Line 9: / Line 9: @@
 <pre>#   hydrate - Jmol script by Ron Mignery
-#   v1.0 beta    9/11/2015
+#   v1.1 beta    4/12/2016 -require latest common includes
+#
 #   View waters of hydration (HOH) iteratively of any model
@@ Line 20: / Line 20: @@
 gSel = ""
 function add_water(idx) {
-     f = _frameID/1000000
+     var f = _frameID/1000000
-     m = _frameID%1000000
+     var m = _frameID%1000000
      var iChain = {atomIndex=idx}.chain
      var ap = {atomIndex=idx}
@@ Line 165: / Line 165: @@
                  halo off
                  display all
-                 unbind all
+                 unbind
                  background echo yellow
                  color echo red
@@ Line 314: / Line 314: @@
      # 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/hydrate - Revision history

Remig at 17:33, 12 April 2016

Remig: Add, remove and view polypeptide waters