User:Remig/plico/convert
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Convert_residue allows the user to change polypeptide or polynucleotide residues from one type to another. When the residue to change is selected with a mouse click, the user is prompted for the amino-acid or nucleotide to replace the selected residue.
The script also allows the user to double-bond or single bond all planars (aromatics, amides, etc) in an amino-acid or nucletotide chain by a shift-click or alt-shift-click respectively. Double-bonding is useful to prevent certain distortions introduced by minimization and allows proper placement of hydrogens with the 'calculate hydrogens' command.
Convert_residue 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 Convert residue Script=script <path to your scripts directory>/convert_residue.spt;plico_convert
saved as plicoConvert.macro in your .jmol/macros directory as described in Macro.
Copy and paste the following to a text editor and save to your scripts directory as convert_residue.spt:
# convert_residue - Jmol script by Ron Mignery
# v1.4 beta 9/11/2015 -use thisModel
#
# Converts a selected residue base from one form to another.
# Alt-Click to select a residue
# Then enter new residue type:
# One of ACDEFGHIKLMNPQRSTUVWXY for polypeptide or
# One of ACGUT for nucleotides
# Or add or remove double bonds from aromatics, amides, and carboxyls
# Click to select a chain (Shift-Click to add, Alt-Shift-Click to remove)
kConvert = 1
gAppendNew = true
g1from3 = {"ALA":"A", "GLX":"B","CYS":"C", "ASP":"D","GLU":"E", "PHE":"F",
"GLY":"G", "HIS":"H","ILE":"I", "LYS":"K","LEU":"L", "MET":"M",
"ASN":"N", "PYL":"O","PRO":"P", "GLN":"Q","ARG":"R", "SER":"S",
"THR":"T", "SEC":"U","VAL":"V", "TRP":"W","UNK":"X", "TYR":"Y", "ASX":"Z"}
function convert_aa(iResno, iChain, newres) {
gBusy = true
background ECHO pink
refresh
gCHAIN = iChain
# Collect orientation
var aO = get_atom_rcn(iResno, iChain, "O")
var aC = get_atom_rcn(iResno, iChain, "C")
var aCA = get_atom_rcn(iResno, iChain, "CA")
var aN = get_atom_rcn(iResno, iChain, "N")
var aNp = {connected(aC) and (atomname="N")}
var aCAp = {connected(aNp) and (atomname="CA")}
var aCxyz = aC.xyz + {0 0 0}
var aOxyz = aO.xyz + {0 0 0}
var angC = angle(aNp, aC, aCA)
var dihedralC = angle(aCAp, aNp, aC, aCA)
var psi = angle(aNp, aC, aCA, aN)
gN = aN.atomno
# Delete the original
delete {(resno=iResno) and (chain=iChain) and thisModel}
# Make a new AA
gA = "data \"append aa\"\n"
# Call gen_aa in ribozyme.spt
gA += gen_aa(iResno, newres);
gA += "end \"append aa\""
gAppendNew = appendNew
set appendNew false
script inline @{gA}
appendNew = gAppendNew
# Recollect data and move backbone to coords of old aa
aO = get_atom_rcn(iResno, iChain, "O")
aC = get_atom_rcn(iResno, iChain, "C")
aCA = get_atom_rcn(iResno, iChain, "CA")
aN = get_atom_rcn(iResno, iChain, "N")
select {(chain=iChain) and (resno=iResno) and thisModel}
var v = aCxyz - aC.xyz
translate Selected @v
var v1=aNp.xyz - aC.xyz
var v2=aCA.xyz - aC.xyz
var axis = cross(v1, v2) + aC.xyz
var curangle = angle(aNp, aC, aCA)
rotateselected @aC @axis @{angC-curangle}
curangle = angle(aCAp, aNp, aC, aCA)
rotateselected @aNp @aC @{dihedralC-curangle}
curangle = angle(aNp, aC, aCA, aN)
rotateselected @aC @aCA @{psi-curangle}
aO.xyz = aOxyz
# Connect the new AA
var aCm = get_atom_rcn(iResno-1, iChain, "C")
connect @aN @aCm
connect @aC @aNp
# Update atomnos
var topdif = {(resno=iResno) and (chain=iChain)
and thisModel}.atomno.max - topno
if (topdif != 0) {
topmax = {(chain=iChain) and thisModel}.atomno.max
for (var i=(topno+1); i <= topmax; i++) {
{(atomno=i) and (chain=iChain) and thisModel}.atomno += topdif
}
}
set echo TOP LEFT
background ECHO yellow
refresh
gBusy = false
}
function atom_rcn_xyz(iResno, iChain, iName, xyz) {
var a = get_atom_rcn(iResno, iChain, iName)
a.xyz = xyz
}
function convert_nt(iResno, iChain, newres) {
gChain1 = iChain
# Collect data
var topno = {(resno=iResno) and (chain=iChain)
and thisModel}.atomno.max + 0
var idmax = {thisModel}.atomIndex.max
var aO4 = get_atom_rcn(iResno, iChain, "O4\'")
if (newres = "") {
newres = aO4.group
}
var aC1 = get_atom_rcn(iResno, iChain, "C1\'")
var aC4 = get_atom_rcn(iResno, iChain, "C4\'")
var aP = get_atom_rcn(iResno, iChain, "P")
var aPxyz = aP.xyz + {0 0 0}
var aOP1xyz = get_atom_rcn(iResno, iChain, "OP1").xyz + {0 0 0}
var aOP2xyz = get_atom_rcn(iResno, iChain, "OP2").xyz + {0 0 0}
var aC1xyz = aC1.xyz + {0 0 0}
var aO4xyz = aO4.xyz + {0 0 0}
var aO3xyz = get_atom_rcn(iResno, iChain, "O3\'").xyz + {0 0 0}
var aC3xyz = get_atom_rcn(iResno, iChain, "C3\'").xyz + {0 0 0}
var aC2xyz = get_atom_rcn(iResno, iChain, "C2\'").xyz + {0 0 0}
var aO2xyz = get_atom_rcn(iResno, iChain, "O2\'").xyz + {0 0 0}
var aC4xyz = aC4.xyz + {0 0 0}
var aC5xyz = get_atom_rcn(iResno, iChain, "C5\'").xyz + {0 0 0}
var aO5xyz = get_atom_rcn(iResno, iChain, "O5\'").xyz + {0 0 0}
var isR = (aC1 and {purine})
var N1or9 = (isR ? "N9" : "N1")
var C6or8 = (isR ? "C8" : "C6")
if (aC1.group = "PSU") {
N1or9 = "C5"
}
var aN = get_atom_rcn(iResno, iChain, N1or9)
var aC = get_atom_rcn(iResno, iChain, C6or8)
var chi = angle(aO4, aC1, aN, aC)
var dist = distance( aC1, aN)
var bang = angle( aO4, aC1, aN)
var bdh = angle( aC4, aO4, aC1, aN)
gNa = aP.atomno
# Delete the original
delete {(resno=iResno) and (chain=iChain) and thisModel}
# Gen NT ==================================================
var isRna = (aO2xyz != -1)
gA = "data \"append nt\"\n"
gA += gen_nt(iResno, newres, isRna, false); # CALL
gA += "end \"append nt\""
gAppendNew = appendNew
set appendNew false
script inline @{gA}
appendNew = gAppendNew
# Recollect data and move new NT to coords of old
isR = ((newres="A") or (newres="G"))
N1or9 = (isR ? "N9" : "N1")
C6or8 = (isR ? "C8" : "C6")
var N3or7 = (isR ? "N7" : "N3")
aN = get_atom_rcn(iResno, iChain, N1or9)
aC = get_atom_rcn(iResno, iChain, C6or8)
var aN3or7 = get_atom_rcn(iResno, iChain, N3or7)
var aC4 = get_atom_rcn(iResno, iChain, "C4\'")
aO4 = get_atom_rcn(iResno, iChain, "O4\'")
aC1 = get_atom_rcn(iResno, iChain, "C1\'")
aP = get_atom_rcn(iResno, iChain, "P")
var aO3 = get_atom_rcn(iResno, iChain, "O3\'")
if (aPxyz != -1) {
aP.xyz = aPxyz
atom_rcn_xyz(iResno, iChain, "OP1", aOP1xyz)
atom_rcn_xyz(iResno, iChain, "OP2", aOP2xyz)
}
else {
delete aP
aP = get_atom_rcn(iResno, iChain, "OP1")
delete aP
aP = get_atom_rcn(iResno, iChain, "OP2")
delete aP
}
aC1.xyz = aC1xyz
aO4.xyz = aO4xyz
aO3.xyz = aO3xyz
atom_rcn_xyz(iResno, iChain, "C3\'", aC3xyz)
atom_rcn_xyz(iResno, iChain, "C2\'", aC2xyz)
atom_rcn_xyz(iResno, iChain, "O2\'", aO2xyz)
aC4.xyz = aC4xyz
atom_rcn_xyz(iResno, iChain, "C5\'", aC5xyz)
atom_rcn_xyz(iResno, iChain, "O5\'", aO5xyz)
# Reconstruct base position on backbone
select ((atomIndex > idmax) and base and thisModel)
color {selected} @gAltScheme
set_distance_atoms( aC1, aN, dist)
set_angle_atoms( aO4, aC1, aN, bang)
set_dihedral_atoms( aC4, aO4, aC1, aN, bdh)
set_angle_atoms( aC1, aN, aC, (isR ? 128.5 : 121.4))
set_dihedral_atoms( aC1, aN, aC, aN3or7, 180.0)
set_dihedral_atoms( aO4, aC1, aN, aC, chi)
# Connect the new NT
var aO3m = get_atom_rcn(iResno-1, iChain, "O3\'")
var aPp = get_atom_rcn(iResno+1, iChain, "P")
connect @aP @aO3m
connect @aO3 @aPp
refresh
gBusy = false
}
function convert_mb() {
if (gBusy == false) {
var idx = _atomPicked
var isAmino = ({(atomIndex=idx) and amino}
or ({atomIndex=idx}.group="SEC")
or ({atomIndex=idx}.group="PYL"))
var isNT = {(atomIndex=idx) and (rna or dna)}
var iResno = {atomIndex=idx}.resno
var iGroup = {atomIndex=idx}.group
var iChain = {atomIndex=idx}.chain
var sels = ""
select {(resno=iResno) and (chain=iChain) and thisModel}
halo on
refresh
if (isAmino) {
if (kPHI) {
script $SCRIPT_PATH$ribozome.spt
if (kPHI) {
prompt ("The Plico script ribozome.spt is required")
quit
}
}
sels = "ABCDEFGHIKLMNOPQRSTUVWXYZ"
var selp = " (enter 1 or 3 characters)"
}
else if (isNT) {
if (kPolymeraze < 1) {
script $SCRIPT_PATH$polymeraze.spt
if (kPolymeraze < 1) {
prompt ("The Plico script polymeraze.spt (1.14+) is required")
quit
}
}
sels = "ACGTU"
selp = " (enter A, C, G, T, or U)"
}
if (sels) {
var ps = format("Change residue %d from %s to ?\n%s",
iResno, iGroup, selp)
var newres = prompt(ps, "")%9999%0
if (isAmino and (newres.size==3)) {
newres = g1from3[newres]
}
else if (newres.size==2) {
newres = newres[2]
}
if ((newres != "") and (newres != "NULL")) {
if (sels.find(newres[1]) > 0) {
gBusy = true
background ECHO pink
refresh
if (isAmino) {
convert_aa(iResno, iChain, newres[1])
}
else {
convert_nt(iResno, iChain, newres[1])
}
update_atomnos(iChain)
set echo TOP LEFT
background ECHO yellow
refresh
}
else {
prompt("Invalid entry")
}
}
}
else {
prompt("Not a polypeptide or polynucleotide")
}
select {(resno=iResno) and (chain=iChain) and thisModel}
halo off
}
}
function double_mb() {
var idx = _atomPicked
var iChain = {atomIndex=idx}.chain
background ECHO pink
refresh
double_bond_planars(iChain, false)
background ECHO yellow
refresh
}
function undouble_mb() {
var idx = _atomPicked
var iChain = {atomIndex=idx}.chain
background ECHO pink
refresh
double_bond_planars(iChain, true)
background ECHO yellow
refresh
}
function convert_exit_mb() {
if (plico_exit()) {
set allowRotateSelected gAllowRotateSelected
set allowMoveAtoms gAllowMoveAtoms
}
}
# Top level of Modify
function plico_convert() {
gBusy = false
gSelsave = {selected}
gPlico = "CONVERT RESIDUE"
# 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 (kNTcommon < 4) {
script $SCRIPT_PATH$plicoNTcommon.spt
if (kNTcommon < 4) {
prompt ("A newer version of plicoNTcommon.SPT is required")
quit
}
}
set echo TOP LEFT
background ECHO yellow
gEcho = ("____CONVERT_RESIDUE____|ALT-CLICK=select residue"+
"|SHIFT-CLICK=add double bonds to chain"+
"|ALT-SHIFT-CLICK=remove double bonds|SHIFT-DOUBLE-CLICK=exit")
echo @gEcho
gChain = ""
gMenuMin = false
unbind
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:convert_mb";
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:double_mb";
bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
bind "ALT-SHIFT-LEFT-CLICK" "+:undouble_mb";
bind "ALT-CTRL-LEFT-CLICK" "align_trna";
bind "SHIFT-DOUBLE" "convert_exit_mb";
bind "LEFT-CLICK" "+:plico_menu_toggle";
}
function connect_res_nt( r5, r3, iChain, del) {
var aO3 = get_atom_rcn(r5, iChain, "O3\'")
var aP = get_atom_rcn(r3, iChain, "P")
if (del) {
connect @aO3 @aP DELETE
}
else {
connect @aO3 @aP
fix_p_res(r3, iChain, false)
}
}
# End of CONVERT_RESIDUE.SPT
