//Jmol predefined set information adapted from JmolConstants.java //Bob Hanson hansonr@stolaf.edu 3:54 PM 12/23/2004 MyDefs=new Array() style=";" nimages=0 _a = specialAtomNames = new Array( //////////////////////////////////////////////////////////////// // The ordering of these entries can be changed ... BUT ... // the offsets must be kept consistent with the ATOMID definitions // below. // // null is entry 0 // The first 32 entries are reserved for null + 31 'distinguishing atoms' // see definitions below. 32 is magical because bits are used in an // int to distinguish groups. If we need more then we can go to 64 // bits by using a long ... but code must change. // // All entries less than 64 are backbone entries // But the number 64 is not magical and could be easily changed //////////////////////////////////////////////////////////////// null, // 0 // protein backbone // "N", // 1 - amino nitrogen "CA", // 2 - alpha carbon "C", // 3 - carbonyl carbon null, // used to be carbonyl oxygen, now can be O or O1 // nucleic acid backbone sugar // "O5'", // 5 - sugar 5' oxygen "C5'", // 6 - sugar 5' carbon "C4'", // 7 - sugar ring 4' carbon "C3'", // 8 - sugar ring 3' carbon "O3'", // 9 - sugar 3' oxygen "C2'", // 10 - sugar ring 2' carbon "C1'", // 11 - sugar ring 1' carbon // Phosphorus is not required for a nucleic group because // at the terminus it could have H5T or O5T ... "P", // 12 - phosphate phosphorus // ... But we need to distinguish phosphorus separately because // it could be found in phosphorus-only nucleic polymers // reserved for future expansion ... lipids & carbohydrates null, null, null, // 13 - 15 null, null, null, null, // 16 - 19 null, null, null, null, // 20 - 23 null, null, null, null, // 24 - 27 null, null, null, null, // 28 - 31 // anything that could be considered part of the 'backbone' // goes in this next group // protein backbone // "OXT", // 32 - second carbonyl oxygen, C-terminus only // protein backbone hydrogens // "H", // 33 - amino hydrogen // these appear on the N-terminus end of 1ALE & 1LCD "1H", // 34 - N-terminus hydrogen "2H", // 35 - second N-terminus Hydrogen "3H", // 36 - third N-terminus Hydrogen "HA", // 37 - H on alpha carbon "1HA", // 38 - H on alpha carbon in Gly only "2HA", // 39 - 1ALE calls the two GLY hdrogens 1HA & 2HA "O", // 40 - carbonyl oxygen "O1", // 41 - carbonyl oxygen in some protein residues (4THN) null, // 42 null, // 43 null, // 44 // Terminal nuclic acid "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P "O5T", // 46 - 5' terminus oxygen which replaces P + O1P + O2P "O1P", // 47 - first equivalent oxygen on phosphorus of phosphate "O2P", // 48 - second equivalent oxygen on phosphorus of phosphate "O4'", // 49 - sugar ring 4' oxygen ... not present in +T ... maybe others "O2'", // 50 - sugar 2' oxygen, unique to RNA // nucleic acid backbone hydrogens // "1H5'", // 51 - first equivalent H on sugar 5' carbon "2H5'", // 52 - second equivalent H on sugar 5' carbon "H4'", // 53 - H on sugar ring 4' carbon "H3'", // 54 - H on sugar ring 3' carbon "1H2'", // 55 - first equivalent H on sugar ring 2' carbon "2H2'", // 56 - second equivalent H on sugar ring 2' carbon "2HO'", // 57 - H on sugar 2' oxygen, unique to RNA "H1'", // 58 - H on sugar ring 1' carbon // "H3T", // 59 - 3' terminus hydrogen // null, // 60 null, // 61 null, // 62 null, // 63 // everything before this (1 - 63, but not 0) is backbone // nucleic acid bases // "N1", // 64 "C2", // 65 "N3", // 66 "C4", // 67 "C5", // 68 "C6", // 69 -- currently defined as the nucleotide wing // this determines the vector for the sheet // could be changed if necessary // pyrimidine O2 // "O2", // 70 // purine stuff // "N7", // 71 "C8", // 72 "N9", // 73 // nucleic acid base ring functional groups // "N4", // 74 - base ring N4, unique to C "N2", // 75 - base amino N2, unique to G "N6", // 76 - base amino N6, unique to A "C5M", // 77 - base methyl carbon, unique to T "O6", // 78 - base carbonyl O6, only in G and I "O4", // 79 - base carbonyl O4, only in T and U "S4", // 80 - base thiol sulfur, unique to thio-U "") GROUPID_PROLINE = 15; GROUPID_PURINE_MIN = 24; GROUPID_PURINE_LAST = 29; GROUPID_PYRIMIDINE_MIN = 30; GROUPID_PYRIMIDINE_LAST = 35; GROUPID_GUANINE = 26; GROUPID_PLUS_GUANINE = 27; GROUPID_GUANINE_1_MIN = 40; GROUPID_GUANINE_1_LAST = 46; GROUPID_GUANINE_2_MIN = 55; GROUPID_GUANINE_2_LAST = 57; GROUPID_AMINO_MAX = 23; GROUPID_SHAPELY_MAX = 36; _g = predefinedGroup3Names = new Array( "", // 0 this is the null group "ALA", // 1 "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", // 15 Proline "SER", "THR", "TRP", "TYR", "VAL", "ASX", // 21 ASP/ASN ambiguous "GLX", // 22 GLU/GLN ambiguous "UNK", // 23 unknown -- 23 // if you change these numbers you *must* update // the predefined sets in script.Token.java "A", // 24 the purines "+A", "G", // 26 "+G", "I", // 28 "+I", "C", // 30 the pyrimidines "+C", "T", // 32 "+T", "U", // 34 "+U", "1MA", // 36 "AMO", "5MC", "OMC", "1MG", // 40 "2MG", "M2G", "7MG", "G7M", "OMG", // 45 "YG", "QUO", "H2U", "5MU", "4SU", // 50 "PSU", "AMP", "ADP", "ATP", "GMP", // 55 "GDP", "GTP", "IMP", "IDP", "ITP", // 60 "CMP", "CDP", "CTP", "TMP", "TDP", // 65 "TTP", "UMP", "UDP", "UTP", // 69 // water && solvent "HOH", // 70 "DOD", // 71 "WAT", // 72 // ions && solvent "PO4", // 73 phosphate ions "SO4", // 74 sulphate ions "") PreDefinedSets=new Array( "// protein related", "protein hardwired", "@amino _g>0 & _g<=23", "@acidic asp,glu", "@basic arg,his,lys", "@charged acidic,basic", "@negative acidic", "@positive basic", "@neutral amino & !(acidic,basic)", "@polar amino & !hydrophobic", "@cyclic his,phe,pro,trp,tyr", "@acyclic amino & !cyclic", "@aliphatic ala,gly,ile,leu,val", "@aromatic his,phe,trp,tyr", "@buried ala,cys,ile,leu,met,phe,trp,val", "@surface !buried", "@hydrophobic ala,gly,ile,leu,met,phe,pro,trp,tyr,val", "@ligand hetero & !solvent", "@mainchain backbone", "@small ala,gly,ser", "@medium asn,asp,cys,pro,thr,val", "@large arg,glu,gln,his,ile,leu,lys,met,phe,trp,tyr", "// nucleic acid related", "nucleic hardwired", "dna hardwired", "rna hardwired", "purine hardwired", "pyrimidine hardwired", "@c nucleic & within(group,_a=74)", "@g nucleic & within(group,_a=75)", "@cg c,g", "@a nucleic & within(group,_a=76)", "@t nucleic & within(group,_a=77)", "@at a,t", "@i nucleic & within(group,_a=78) & !g", "@u nucleic & within(group,_a=79) & !t", "@tu nucleic & within(group,_a=80)", "// solvent related", "@solvent _g>=70 & _g<=74", // water or ions "@hoh water", "@water _g>=70&_g<=72", "@ions _g=70,_g=71", "// structure related", "@alpha _a=2", "@backbone (protein,nucleic) & _a>0 & _a<=63", "@sidechain (protein,nucleic) & !backbone", "@base nucleic & !backbone", "@turn _structure=1", "@sheet _structure=2", "@helix _structure=3", "@bonded _bondedcount>0", "hetero hardwired", "") function adddef(skey,sdef,itype){ var i=MyDefs.length MyDefs[i]=new Array() MyDefs[i].skey=skey MyDefs[i].sdef=sdef MyDefs[i].itype=itype } function getPreDefined(){ var sout="" var S=new Array() var sinfo="" var skey="" var sdef="" var pt=0 adddef("groups","",0) for(var i=0;i<_g.length;i++){ sinfo=_g[i] if(sinfo){ adddef(sinfo,sinfo,2) } } for(var i=0;i=0)sdef=skey adddef(skey,sdef,1) }else if(sdef=="hardwired"){ adddef(skey,skey,2) } } } }getPreDefined() function showdefs(){ var sout="" nimages=0 for(var i=0;i

" return sout } function showthedef(n,si,delay){ if(delay==2){ delay=0 var d=document.getElementById("select"+n) si=d[d.selectedIndex].value } if(delay){ setTimeout("showthedef("+n+","+si+",2)",100) return } var ithis=parseInt(si+"") if(ithis<0)n=-1 for(var i=0;i=0?"rockets off;select "+MyDefs[ithis].skey+style+"#"+MyDefs[ithis].sdef:"")) }