Remig at 17:36, 12 April 2016

2016-04-12T17:36:08Z

Remig: Some useful scripts for manually folding polypeptides

2015-09-11T16:02:35Z

Some useful scripts for manually folding polypeptides

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'''Utils''' presents a menu of actions potentially useful for manual folding of polypeptides:

Hover text may be enhanced to include atomIndex values.

All collisions may be listed.

Dispersion bonds contributing to secondary structure (displayed as grey arrows between atoms on residues within 4 AAs of eachother) may be toggled on and off.

Dispersion bonds contributing to tertiary structure (displayed as yellow arrows between atoms outside 4 AAs of eachother) may be toggled on and off.

All dispersion bonds may be cleared.

Paired coils may be presented in a format that highlights the forces pairing them: cartoon backbone, ball-and-stick side-chains, hbonds, and halos on CB atoms.

Utils 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 Utilities
Script=script <path to your script directory>/utils.spt;plico_utils
</pre>saved as utilities.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 utils.spt.

<pre># utils - Jmol script by Ron Mignery
# v1.0 beta 9/11/2015
#
gE = false
gR = false

function is_collision_in_select() {
is = false
var cAtoms = ({})
var iChain = {selected}.chain
for (var no = {selected}.min.atomno; no <= {selected}.max.atomno; no++) {
a = {(atomno=no) and (chain=iChain) and thisModel}
if (a) {
is = true
break
}
}
return is
}

# A handy debug routine
function cc {
print count_collisions(true)
}

function super_coil_prompt() {
prompt("TBD")
}

function show_interchain_vbonds() {
var pc = 0
if (not gBusy) {
var selsave = {selected}
select {visible}
gBusy = true
background ECHO pink
refresh
if (gE) {
print "Hiding intERchain dispersion bonds"
gE = false
draw ID "vdwe*" delete
}
else {
print "Showing intERchain dispersion bonds"

# For all visible atoms
for (var i = {*}.atomIndex.min; i <= {*}.atomIndex.max; i++) {
var a = {atomIndex=i}
if ((a.group != "hoh") and (a.element != "H")) {
var iChain = a.chain

# If side chain carbon (or sulfur)
if ({a and sidechain and not hydrogen} and a.selected) {
var nset = {within(104, VDW, a)
and ((chain != iChain) or (not within(4,GROUP, a)))
and not hoh and not hydrogen and selected}
for (var j = 1; j <= nset.size; j++) {
var id = format("vdwe%d.%d", i, j)
draw ID @id arrow @{a} @{nset[j]}
pc++
}
}
}
}
gE = true
}
background ECHO lightgrey
refresh
select selsave
gBusy = false
}
return pc
}

function show_intrachain_vbonds() {
if (not gBusy) {
var selsave = {selected}
select {visible}
gBusy = true
var pc = 0
background ECHO pink
refresh

if (gR) {
print "Hiding intRAchain dispersion bonds"
gR = false
draw ID "vdwr*" delete
}
else {
print "Showing intRAchain dispersion bonds"

# For all visible atoms
for (var i = {*}.atomIndex.min; i <= {*}.atomIndex.max; i++) {
var a = {atomIndex=i}
var iChain = a.chain

if ({a and sidechain and not hydrogen and selected}) {
var nset = {within(100, VDW, a) and within(4,GROUP, a)
and not connected(a) and not connected(connected(a))
and not hydrogen and (chain = iChain) and selected}
for (var j = 1; j <= nset.size; j++) {
var id = format("vdwr%d.%d", i, j)
draw ID @id arrow @{a} @{nset[j]}
pc++
}
}
}
color $vdwr* lightblue
gR = true
}
background ECHO lightgrey
refresh
select selsave
gBusy = false
}
return pc

}

function calculate_cb(resmin, resmax, ichain, d) {

# For all atoms in range
for (var i = {(resno=resmin) and (chain=ichain)}.atomno.min;
i <= {(resno=resmax) and (chain=ichain)}.atomno.max; i++) {
var a = {(atomno=i) and (chain=ichain)}

# If CB
if (a.atomName == "CB") {

# If within(d, a) and cb
var nset = {within(@d, a) and (atomName = "CB") and not a}
for (var j = 1; j <= nset.size; j++) {
measure @{nset[j]} @a
}
}
}
}

function show_alpha_pairs() {
if (not gBusy) {
gBusy = true
background echo pink
refresh
print "Backbone cartoon, sidechain ball-and-stick, hbonds on, halo on CBs"
select all
calculate STRUCTURE DSSP
cartoons only
color structure
select {sidechain}
wireframe -0.1
spacefill 23%
color jmol
select {atomName="CB"}
halo on
set hbondsRasmol off
select all
calculate hbonds
background echo lightgrey
refresh
gBusy = false
}
}

function utils_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:
print "hover++"
hi()
break
case 2:
print "Counting collisions"
cc()
break
case 3:
print "showing interchain D bonds"
print show_interchain_vbonds()
break
case 4:
print "showing intrachain D bonds"
print show_intrachain_vbonds()
break
case 5:
print "Hiding all D bonds"
draw ID "vdw*" delete
gE = false
gR = false
break
case 6:
print "Show alpha chain pairs"
show_alpha_pairs()
break
case 7:
utils_exit()
break
}
}
}

# Top level of utils
function plico_utils() {

# 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 = "UTILS"
plico_prelim(false, false)
gE = false
gR = false

gEcho="______Menu_______|Hover++|List collisions|Show intERchain D bonds|" +
"Show intRAchain D bonds|Hide all D bonds|Show alpha pairs| BACK"
set echo top left
color echo black
background echo lightgrey
echo @gEcho

bind "SHIFT-DOUBLE" "utils_exit";
bind "LEFT-CLICK" "+:plico_menu_toggle";
bind "LEFT-CLICK" "+:utils_click_mb";

}

function utils_exit() {
if (plico_exit(false)) {
display all
}
}

# End of UTILS.SPT
</pre>

User:Remig/plico/utilities - Revision history

Remig at 17:36, 12 April 2016

Remig: Some useful scripts for manually folding polypeptides