Difference between revisions of "User:Remig/plico/remap"
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Copy and paste the following to a text editor and save to your scripts directory as remap.spt: | Copy and paste the following to a text editor and save to your scripts directory as remap.spt: | ||
<pre># remap - Jmol script by Ron Mignery | <pre># remap - Jmol script by Ron Mignery | ||
− | # v1. | + | # v1.10 beta 4/12/2016 -require latest common includes |
# | # | ||
# Calculate or change polypeptide chain, atom number, residue names and/or residue | # Calculate or change polypeptide chain, atom number, residue names and/or residue | ||
Line 90: | Line 90: | ||
# Prompt for new designators | # Prompt for new designators | ||
− | f = {atomIndex=n0idx}.file | + | var f = {atomIndex=n0idx}.file |
− | m = {atomIndex=n0idx}.model | + | var m = {atomIndex=n0idx}.model |
var iResno = {atomIndex=n0idx}.resno | var iResno = {atomIndex=n0idx}.resno | ||
var iChain = {atomIndex=n0idx}.chain | var iChain = {atomIndex=n0idx}.chain | ||
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# 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 |
Latest revision as of 17:17, 12 April 2016
Remap allows you to change the chain ID, atom numbers and/or residue numbers of a polypeptide chain by mouse actions. It also calculates group values [amino acid names (GLY, THR, etc.)]. Finally it prints the 1 char resultant string to the console.
When you click on a polypeptide chain, it gives the current chain ID, residue, residue number and atom number of the most nward atom in that chain. You may then edit any value (except residue). Remap then remaps the entire chain based on those values by conventional increments and identifies each amino acid residue.
Note that it will also remove all waters, hydrogens and %B alternates when any chain is updated.
Remap 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 Remap Script=script <path to your scripts directory>/remap.spt;plico_remap
saved as plicoRemap.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 remap.spt:
# remap - Jmol script by Ron Mignery # v1.10 beta 4/12/2016 -require latest common includes # # Calculate or change polypeptide chain, atom number, residue names and/or residue # numbers and print the resultant 1 char string # gAppendNew = false gBusy = false # Search for N-C-C-0 function get_bb_nward_ca_idx(idx) { if ({atomIndex=idx}.element == "N") { var c1 = (connected({atomIndex=idx}) and not {hydrogen}) for (var i1 = 1; i1 <= c1.size; i1++) { if (c1[i1].element == "C") { var c2 = (connected({atomIndex=@{c1[i1].atomIndex}}) and not {hydrogen}) for (var i2 = 1; i2 <= c2.size; i2++) { if (c2[i2].element == "C") { var c3 = (connected({atomIndex=@{c2[i2].atomIndex}}) and not {hydrogen}) for (var i3 = 1; i3 <= c3.size; i3++) { if (c3[i3].element == "O") { return c1[i1].atomIndex } } } } } } } return -1 } # Find N-terminal N function find_n0_idx(aIdx) { select {atomIndex=aIdx} var sSet = {selected} while (sSet) { for (var i = 1; i <= sSet.size; i++) { var idx = sSet[i].atomIndex var caIdx = get_bb_nward_ca_idx(idx) if (caIdx >= 0) { var cset = connected({atomIndex=idx}) and not {hydrogen} var ccset = connected(cset) and not {hydrogen} if (cset.size < 2) { return idx #*** } else if (({ccset and {carbon}}.size = 3) and (ccset.size == 4)) { return idx #*** } } } # endfor sSet = connected({selected}) and not {selected} and not {hydrogen} select {selected} or sSet } # endwhile return -1 } # Bound to ALT-LEFT-CLICK by plico_remap function remap_cargo_mb() { var idx =_atomPicked if ({atomIndex=idx}.element == "H") { idx = connected({atomIndex=idx})[1].atomIndex } # If n-terminal N can be found var n0idx = find_n0_idx(idx) var isValid = false var newResno = 1 var newChain = "A" var newAtomno = 1 if (n0idx >= 0) { # Prompt for new designators var f = {atomIndex=n0idx}.file var m = {atomIndex=n0idx}.model var iResno = {atomIndex=n0idx}.resno var iChain = {atomIndex=n0idx}.chain var iNo = {atomIndex=n0idx}.atomno select {thisModel} color {selected} @gScheme select {(chain=iChain) and thisModel} color {selected} @gAltScheme refresh var p = prompt("Enter n-terminal atom designator as\n" + " <resno>:<chain>.N#<atomno>", format("%d:%s.N#%d", iResno, iChain, iNo)%0) # If valid var iColon = p.find(":") if (iColon > 0) { var iDot = p.find(".") if (iDot > 0) { var iHash = p.find("#") if (iHash > 0) { newResno = 0 + (p[1][iColon-1]) newChain = p[iColon+1][iDot-1] newAtomno = 0 + (p[iHash+1][0]) if ((newResno > 0) and (newChain.size == 1) and (newAtomno > 0)) { isValid = true } } } } } if (isValid) { delete {hydrogen and thisModel} delete {hoh and thisModel} delete %B and thisModel ssbonds off # Build inline pdb file var ls = "data \"append remap\"\n" var rs = "" var ls1 = format("%s:", newChain) select {atomIndex=n0idx} var cSet = {selected} var newAtomName = "N" var newGroup = "UNK" var s1 = "X" var newGreek = "" var newCount = "" var isCB = false var nIdx = n0idx var proDidx = -1 var oxtIdx = -1 while ((nIdx >= n0idx) or (cSet)) { var s = array(1, 2, 3) var pTrp = 0 if (cSet.size == 0) { ls += rs.replace("UNK", newGroup).replace(" SeG" , " SeG ") ls1 += s1 rs = "" newResno++ nIdx = -1 proIdx = -1 newGroup = "UNK" s1 = "X" newAtomName = "N" isCB = false } else if (cSet.size == 1) { if (newAtomName == "N") { newGreek = "" newAtomName = "CA" } else if (newAtomName == "CA") { newGreek = "A" newAtomName = "C" } else if (newAtomName == "C") { newGroup = "GLY" s1 = "G" newGreek = "" newAtomName = "O" } else if (newAtomName == "CB") { if (cSet[1].element == "C") { newGroup = "ALA" # for now s1 = "A" newGreek = "B" } newAtomName = "XG" } else if (newAtomName == "XG") { if (proDidx >= 0) { newGroup = "PRO" s1 = "P" proDidx = -1 } if (cSet[1].element == "O") { # SER CYS SEC newGroup = "SER" s1 = "S" } else if (cSet[1].element == "S") { newGroup = "CYS" s1 = "C" } else if (cSet[1].element == "Se") { newGroup = "SEC" s1 = "U" } newGreek = "G" newAtomName = "XD" } else if (newAtomName == "XD") { if (newGroup == "VAL") { newGroup = "ILE" s1 = "I" newCount = "1" } newGreek = "D" newAtomName = "XE" } else if (newAtomName == "XE") { newGroup = "MET" s1 = "M" newGreek = "E" newAtomName = "XZ" } else if (newAtomName == "XZ") { if (cSet[1].element == "N") { newGroup = "LYS" s1 = "K" } else { newGroup = "PHE" # for now s1 = "F" } newGreek = "Z" newAtomName = "XH" } else if (newAtomName == "XH") { if (cSet[1].element == "O") { newGroup = "TYR" s1 = "Y" } else { newGroup = "TRP" # for now s1 = "W" newCount = "2" } newGreek = "H" newAtomName = "N" } } else if (cSet.size == 2) { var hasN = ((cSet[1].element == "N") or (cSet[2].element == "N")) var hasO = ((cSet[1].element == "O") or (cSet[2].element == "O")) # If CA 2 if (newAtomName == "CA") { var iKeep = -1 for (var i = 1; i <= cSet.size; i++) { if (connected(cSet[i]) > 2) { iKeep = i } else { proDidx = cSet[i].atomIndex cSet[i].selected = false } } cSet = cSet[iKeep] newGroup = "PRO" s1 = "P" newGreek = "A" newAtomName = "C" } # Else if C or CB 2 else if (newAtomName == "C") { for (var i = 1; i <= cSet.size; i++) { # If it connects O and (N or O) var tSet = (connected(cSet[i]) and not {selected}) var oCount = 0 var nCount = 0 for (var j = 1; j <= tSet.size; j++) { oCount += ((tSet[j].element == "O") ? 1 : 0) nCount += ((tSet[j].element == "N") ? 1 : 0) } if ((nCount > 0) or (oCount > 1)) { # C newGreek = "" newAtomName = "O" } else { # CB isCB = true cSet[i].selected = false cSet = (cSet and not cSet[i]) continue } } # endfor } # Else if O or N 2 else if (newAtomName == "O") { var iKeep = -1 for (var i = 1; i <= cSet.size; i++) { if (cSet[i].element != "O") { if (cSet[i].element == "N") { nIdx = cSet[i].atomIndex } cSet[i].selected = false } else { iKeep = i } } cSet = cSet[iKeep] newGreek = "" newAtomName = (isCB ? "CB" : "N") } # Else if N or CB 2 else if (newAtomName == "CB") { for (var i = 1; i <= cSet.size; i++) { if (cSet[i].element != "C") { nIdx = cSet[i].atomIndex cSet[i].selected = false continue } newGreek = "B" newAtomName = "XG" } # endfor } # Else if XG or XGn 2 else if (newAtomName == "XG") { # VAL THR ILE newGroup = (hasO ? "THR" : "VAL") s1 = (hasO ? "T" : "V") newGreek = "G" newAtomName = "XD" } # Else if XD or XDn 2 else if (newAtomName == "XD") { # LEU ASP ASN var cTrp = (connected(cSet[2]) and not {selected}) var sTrp = ((trp) ? (trp[1].element=="N") : false) if ((cSet[2].element != "C") or sTrp or ((connected(cSet[1]) and not {selected}).size == 0)) { bRev = true } if ((cSet[2].element == "O") or (cSet[1].element == "N") or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { bRev = true } if (hasN) { if (hasO) { newGroup = "ASN" s1 = "N" } else { newGroup = "HIS" s1 = "H" } } else if (hasO) { newGroup = "ASP" s1 = "D" } else { newGroup = "LEU" # for now s1 = "L" } newGreek = "D" newAtomName = "XE" } # Else if XE or XEn 2 else if (newAtomName == "XE") { # GLU GLN HIS if ((cSet[2].element == "O") or (cSet[1].element == "N") or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { bRev = true } if (hasO) { if (hasN) { newGroup = "GLN" s1 = "Q" } else { newGroup = "GLU" s1 = "E" } } newGreek = "E" newAtomName = "XZ" } # Else if XZ 2 else if (newAtomName == "XZ") { # ARG if (newGroup == "TRP") { pTrp = 1 } newGreek = "Z" newAtomName = "XH" } # Else if XH 2 else if (newAtomName == "XH") { # ARG newGroup = "ARG" s1 = "R" newGreek = "H" newAtomName = "N" } } # Else cSet.size = 3 else { # If O if (newAtomName == "O") { var oCount = 0 var iKeep = -1 for (var i = 1; i <= cSet.size; i++) { if (cSet[i].element != "O") { if (cSet[i].element == "N") { nIdx = cSet[i].atomIndex } cSet[i].selected = false } else { oCount++ if (iKeep < 0) { iKeep = i } else { oxtIdx = cSet[i].atomIndex } } } cset = cSet[iKeep[1]] newGreek = "" newAtomName = (isCB ? "CB" : "N") } else if (newAtomName == "CA") { # PRO var iKeep = -1 for (var i = 1; i <= cSet.size; i++) { if (connected(cSet[i]) > 2) { iKeep = i } } cSet = cSet[iKeep] newGreek = "A" newAtomName = "C" } else if (newAtomName == "XE") { # TRP for (var i = 1; i <= cSet.size; i++) { if (cSet[i].element == "N") { s[1] = i } else if (connected(cSet[i]) > 2) { s[2] = i } else { s[3] = i } } newGroup = "TRP" s1 = "W" newGreek = "E" newAtomName = "XZ" } else { } } for (var i = 1; i <= cSet.size; i++) { rs += format("ATOM %5d %-4sUNK ", newAtomNo, (cSet[s[i]].element + newGreek + ((cSet.size > 1) ? (i+pTrp) : newCount))) rs += format("%s%4d %8.3f", newChain, newResno, cSet[s[i]].x) rs += format("%8.3f%8.3f\n", cSet[s[i]].y, cSet[s[i]].z) if (newGreek == "XT") { newGreek == "" } newAtomno++ } newCount = "" cSet = (connected({selected}) and not {selected} and not {atomIndex=@nIdx} and not {atomIndex=proDidx}) select ({selected} or cSet and not {atomIndex=nIdx} and not {atomIndex=proDidx}) } # endwhile # Replace chain with new chain if (oxtIdx >= 0) { rs += format("ATOM %5d OXT UNK %s", newAtomNo, newChain) rs += format("%4d %8.3f", newResno, {atomIndex=oxtIdx}.x) rs += format("%8.3f%8.3f\n", {atomIndex=oxtIdx}.y, {atomIndex=oxtIdx}.z) } ls += rs.replace("UNK", newGroup).replace(" SeG" , " SeG ") ls1 += s1 delete {selected} ls += "end \"append remap\"" gAppendNew = appendNew set appendNew false script inline @{ls} set appendNew gAppendNew var xx = {element="Xx"} for (var i = 1; i <= xx.size; i++) { connect 1.8 {atomindex=@{xx[i].atomIndex}} } ssbonds on gEcho += format("|Chain %s has been rebuilt", newChain) set echo TOP LEFT echo @gEcho print ls1 } else { color {selected} @gScheme } } # Top level of Remap function plico_remap() { # 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 } } gPlico = "Remap" plico_prelim(false, true) gEcho = "_______REMAP_______|ALT-CLICK=select chain|SHIFT-DOUBLE-CLICK=exit" echo @gEcho set picking ON bind "ALT-LEFT-CLICK" "_pickAtom"; bind "ALT-LEFT-CLICK" "+:remap_cargo_mb"; bind "SHIFT-DOUBLE" "plico_exit(true)"; bind "LEFT-CLICK" "+:plico_menu_toggle"; } # End of REMAP.SPT