icn3d 3.54.6 → 3.54.8

package/icn3d.js

@@ -179,7 +179,8 @@ $NGL_shaderTextHash['SphereImpostor.frag'] = ["#define STANDARD",
 "                float depth = gl_FragCoord.z / gl_FragCoord.w;",
 "            #endif",
 "            #ifdef FOG_EXP2",
-"                float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"                //float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"                float fogFactor = ( 1.0 - exp2( - fogDensity * fogDensity * depth * depth * 1.442695 ) );",
 "            #else",
 "                float fogFactor = smoothstep( fogNear, fogFar, depth );",
 "            #endif",
@@ -643,7 +644,8 @@ $NGL_shaderTextHash['CylinderImpostor.frag'] = ["#define STANDARD",
 "                float depth = gl_FragCoord.z / gl_FragCoord.w;",
 "            #endif",
 "            #ifdef FOG_EXP2",
-"                float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"                //float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"                float fogFactor = ( 1.0 - exp2( - fogDensity * fogDensity * depth * depth * 1.442695 ) );",
 "            #else",
 "                float fogFactor = smoothstep( fogNear, fogFar, depth );",
 "            #endif",
@@ -2613,13 +2615,33 @@ var CIFTools;
         /**
          * Options for filling the unit cell of a core CIF by lattice translation
          * (applied after the symmetry operators have generated the contents of one cell).
-         *   nx, ny, nz : number of unit cells along a, b, c (supercell); default 1 1 1
-         *   boundary   : also emit the periodic image of every atom lying on a cell face/edge/corner
-         *                (e.g. NaCl -> 14 Na + 13 Cl instead of 4 Na + 4 Cl); default true.
-         *                Set to false to get the original behavior (atoms wrapped into [0,1) only).
-         * Usage (before loading the file):  CIFTools.Text.coreCifOptions = {nx: 2, ny: 2, nz: 2, boundary: true};
+         *   nx, ny, nz     : number of unit cells along a, b, c (supercell); default 1 1 1
+         *   wholeMolecules : keep every molecule / discrete chemical species intact. Atoms are grouped into
+         *                    bonded fragments (covalent radii + bondTolerance, periodic), each fragment is
+         *                    "unwrapped" so that it is contiguous (it may stick out of the unit cell), and the
+         *                    fragment is placed in the cell that contains its centre. Fragments that are
+         *                    infinite (chains, layers, frameworks, ionic lattices such as NaCl) cannot be made
+         *                    whole and are handled as before (wrapped into the cell, see 'boundary'). default true
+         *   bondTolerance  : extra distance (Angstrom) added to the sum of covalent radii when detecting bonds; default 0.4
+         *   boundary       : for atoms that are NOT part of a whole molecule, also emit the periodic image of every
+         *                    atom lying on a cell face/edge/corner (e.g. NaCl -> 14 Na + 13 Cl instead of 4 Na + 4 Cl);
+         *                    default true.
+         * Usage (before loading the file):  CIFTools.Text.coreCifOptions = {nx: 2, ny: 2, nz: 2, wholeMolecules: true};
          */
-        Text.coreCifOptions = { nx: 1, ny: 1, nz: 1, boundary: true };
+        Text.coreCifOptions = {
+            nx: 1, ny: 1, nz: 1,
+            wholeMolecules: true,   // new; set false for the old wrapped behaviour
+            bondTolerance: 0.4,     // new; raise it if bonds are missed, lower it if unrelated atoms get joined, default 0.4
+            boundary: true
+        };
+        // covalent radii (Angstrom, Cordero et al. 2008) used for bond detection
+        var coreCovRadii = { H: 0.31, D: 0.31, He: 0.28, Li: 1.28, Be: 0.96, B: 0.84, C: 0.76, N: 0.71, O: 0.66, F: 0.57, Ne: 0.58,
+            Na: 1.66, Mg: 1.41, Al: 1.21, Si: 1.11, P: 1.07, S: 1.05, Cl: 1.02, Ar: 1.06, K: 2.03, Ca: 1.76, Sc: 1.70, Ti: 1.60, V: 1.53,
+            Cr: 1.39, Mn: 1.39, Fe: 1.32, Co: 1.26, Ni: 1.24, Cu: 1.32, Zn: 1.22, Ga: 1.22, Ge: 1.20, As: 1.19, Se: 1.20, Br: 1.20, Kr: 1.16,
+            Rb: 2.20, Sr: 1.95, Y: 1.90, Zr: 1.75, Nb: 1.64, Mo: 1.54, Tc: 1.47, Ru: 1.46, Rh: 1.42, Pd: 1.39, Ag: 1.45, Cd: 1.44, In: 1.42,
+            Sn: 1.39, Sb: 1.39, Te: 1.38, I: 1.39, Xe: 1.40, Cs: 2.44, Ba: 2.15, La: 2.07, Ce: 2.04, Pr: 2.03, Nd: 2.01, Sm: 1.98, Eu: 1.98,
+            Gd: 1.96, Tb: 1.94, Dy: 1.92, Ho: 1.92, Er: 1.89, Tm: 1.90, Yb: 1.87, Lu: 1.87, Hf: 1.75, Ta: 1.70, W: 1.62, Re: 1.51, Os: 1.44,
+            Ir: 1.41, Pt: 1.36, Au: 1.36, Hg: 1.32, Tl: 1.45, Pb: 1.46, Bi: 1.48 };
         // g: fractional coordinates wrapped into [0,1). Returns all translated copies of g.
         function coreLatticeImages(g, nx, ny, nz, bBoundary) {
             var eps = 1e-3, n = [nx, ny, nz], ranges = [], out = [], k, i, r, x, y, z;
@@ -2635,6 +2657,60 @@ var CIFTools;
                         out.push([ranges[0][x], ranges[1][y], ranges[2][z]]);
             return out;
         }
+        /**
+         * Group atoms (fractional coordinates wrapped into the cell) into bonded fragments, taking periodic
+         * images into account. Every atom of a fragment gets an integer lattice translation T so that
+         * (g + T) forms a contiguous molecule. A fragment that reaches its own periodic image
+         * (chain / layer / framework) is flagged as infinite.
+         *   atoms : [{el, g:[fx,fy,fz]}]   toCart : fractional -> Cartesian (linear part only)
+         *   h     : interplanar spacings of the cell along a, b, c   tol : bond tolerance (Angstrom)
+         */
+        function coreFindMolecules(atoms, toCart, h, tol) {
+            var N = atoms.length, nb = [], rad = [], i, j, k, e, m, q;
+            for (i = 0; i < N; i++) { nb.push([]); rad.push(coreCovRadii[atoms[i].el] || 1.5); }
+            for (i = 0; i < N; i++) {
+                for (j = i; j < N; j++) {
+                    var d = [atoms[j].g[0] - atoms[i].g[0], atoms[j].g[1] - atoms[i].g[1], atoms[j].g[2] - atoms[i].g[2]];
+                    var rc = rad[i] + rad[j] + tol, cand = [[], [], []], dt, t;
+                    for (k = 0; k < 3; k++) {
+                        var base = -Math.round(d[k]);
+                        for (dt = -1; dt <= 1; dt++) {
+                            t = base + dt;
+                            if (Math.abs(d[k] + t) * h[k] <= rc) cand[k].push(t);
+                        }
+                    }
+                    for (var a = 0; a < cand[0].length; a++) for (var b = 0; b < cand[1].length; b++) for (var c = 0; c < cand[2].length; c++) {
+                        var tv = [cand[0][a], cand[1][b], cand[2][c]];
+                        if (i === j) { // bond to own image: record each translation pair only once
+                            if (tv[0] === 0 && tv[1] === 0 && tv[2] === 0) continue;
+                            if (tv[0] < 0 || (tv[0] === 0 && (tv[1] < 0 || (tv[1] === 0 && tv[2] < 0)))) continue;
+                        }
+                        var cc = toCart([d[0] + tv[0], d[1] + tv[1], d[2] + tv[2]]);
+                        var d2 = cc[0] * cc[0] + cc[1] * cc[1] + cc[2] * cc[2];
+                        if (d2 < rc * rc && d2 > 0.25) { // > 0.5 A: closer atoms are disorder alternatives, not bonds
+                            nb[i].push({ j: j, t: tv });
+                            nb[j].push({ j: i, t: [-tv[0], -tv[1], -tv[2]] });
+                        }
+                    }
+                }
+            }
+            var T = new Array(N), comps = [], s, queue, members, infinite, cur, tj, o;
+            for (s = 0; s < N; s++) {
+                if (T[s]) continue;
+                T[s] = [0, 0, 0]; queue = [s]; members = [s]; infinite = false;
+                for (q = 0; q < queue.length; q++) {
+                    cur = queue[q];
+                    for (e = 0; e < nb[cur].length; e++) {
+                        o = nb[cur][e];
+                        tj = [T[cur][0] + o.t[0], T[cur][1] + o.t[1], T[cur][2] + o.t[2]];
+                        if (!T[o.j]) { T[o.j] = tj; queue.push(o.j); members.push(o.j); }
+                        else if (T[o.j][0] !== tj[0] || T[o.j][1] !== tj[1] || T[o.j][2] !== tj[2]) infinite = true;
+                    }
+                }
+                comps.push({ members: members, infinite: infinite });
+            }
+            return { T: T, comps: comps };
+        }
         function convertCoreCif(data) {
             var tk = coreTokens(data), i = 0, n = tk.length, single = {}, loops = [], name = 'data_core', t, cols, rows, cur;
             function isTag(x) { return x && !x.t && x.v.charAt(0) === '_'; }
@@ -2688,12 +2764,21 @@ var CIFTools;
                 '_atom_site.label_comp_id', '_atom_site.label_asym_id', '_atom_site.label_entity_id', '_atom_site.label_seq_id',
                 '_atom_site.Cartn_x', '_atom_site.Cartn_y', '_atom_site.Cartn_z', '_atom_site.occupancy', '_atom_site.B_iso_or_equiv',
                 '_atom_site.auth_seq_id', '_atom_site.auth_asym_id', '_atom_site.pdbx_PDB_model_num');
-            var serial = 0, seen = [], r, s, f, g, k, dup, j, sym, el, lab, cart;
+            var serial = 0, r, s, f, g, k, dup, j, sym, el, lab, cart;
             var o = Text.coreCifOptions || {}, images, im;
             var opt = {
                 nx: Math.max(1, parseInt(o.nx) || 1), ny: Math.max(1, parseInt(o.ny) || 1), nz: Math.max(1, parseInt(o.nz) || 1),
-                boundary: (o.boundary === undefined) ? true : !!o.boundary
+                boundary: (o.boundary === undefined) ? true : !!o.boundary,
+                wholeMolecules: (o.wholeMolecules === undefined) ? true : !!o.wholeMolecules,
+                bondTolerance: (o.bondTolerance === undefined || isNaN(parseFloat(o.bondTolerance))) ? 0.4 : parseFloat(o.bondTolerance)
             };
+            function emit(at, frac) {
+                var cart = toCart(frac);
+                out.push(['HETATM', ++serial, at.el, at.lab, '.', 'MOL', 'A', 1, '.', cart[0].toFixed(3), cart[1].toFixed(3), cart[2].toFixed(3),
+                    at.occ, '0.00', 1, 'A', 1].join(' '));
+            }
+            // 1) all symmetry-generated atoms of one cell, wrapped into [0,1)
+            var list = [];
             for (r = 0; r < atoms.rows.length; r++) {
                 var row = atoms.rows[r];
                 if (get(row, '_atom_site_calc_flag') === 'dum') continue; // dummy atoms
@@ -2702,6 +2787,7 @@ var CIFTools;
                 sym = get(row, '_atom_site_type_symbol'); if (sym === '?') sym = lab;
                 el = (sym.match(/^[A-Za-z]{1,2}/) || ['X'])[0];
                 el = el.charAt(0).toUpperCase() + el.substr(1).toLowerCase();
+                var occ = coreToNumber(get(row, '_atom_site_occupancy') === '?' ? 1 : get(row, '_atom_site_occupancy'));
                 var mySeen = [];
                 for (s = 0; s < symops.length; s++) {
                     g = symops[s](f).map(function (v) { return v - Math.floor(v + 1e-6); });
@@ -2711,15 +2797,51 @@ var CIFTools;
                     }
                     if (dup) continue;
                     mySeen.push(g);
-                    // fill the cell (and optional supercell) by lattice translation of the symmetry-generated site
-                    images = coreLatticeImages(g, opt.nx, opt.ny, opt.nz, opt.boundary);
-                    for (im = 0; im < images.length; im++) {
-                        cart = toCart(images[im]);
-                        out.push(['HETATM', ++serial, el, lab, '.', 'MOL', 'A', 1, '.', cart[0].toFixed(3), cart[1].toFixed(3), cart[2].toFixed(3),
-                            coreToNumber(get(row, '_atom_site_occupancy') === '?' ? 1 : get(row, '_atom_site_occupancy')), '0.00', 1, 'A', 1].join(' '));
+                    list.push({ el: el, lab: lab, occ: occ, g: g });
+                }
+            }
+            // 2) emit them, either as whole molecules or simply wrapped into the cell
+            var mol = null;
+            if (opt.wholeMolecules && list.length) {
+                var Vc = a * b * cc * vol, sinal = Math.sqrt(1 - cosa * cosa), sinbe = Math.sqrt(1 - cosb * cosb);
+                var hh = [Vc / (b * cc * sinal), Vc / (a * cc * sinbe), Vc / (a * b * sing)];
+                if (isFinite(hh[0] + hh[1] + hh[2]) && hh[0] > 0 && hh[1] > 0 && hh[2] > 0) mol = coreFindMolecules(list, toCart, hh, opt.bondTolerance);
+            }
+            var ci, m, at, ix, iy, iz, mean, shift;
+            if (mol) {
+                for (ci = 0; ci < mol.comps.length; ci++) {
+                    var comp = mol.comps[ci];
+                    if (comp.infinite) { // cannot be made whole: wrap into the cell as before
+                        for (m = 0; m < comp.members.length; m++) {
+                            at = list[comp.members[m]];
+                            images = coreLatticeImages(at.g, opt.nx, opt.ny, opt.nz, opt.boundary);
+                            for (im = 0; im < images.length; im++) emit(at, images[im]);
+                        }
+                        continue;
+                    }
+                    // contiguous molecule: place it in the cell that holds its centre, keep all atoms together
+                    mean = [0, 0, 0];
+                    for (m = 0; m < comp.members.length; m++) {
+                        at = list[comp.members[m]];
+                        for (k = 0; k < 3; k++) mean[k] += (at.g[k] + mol.T[comp.members[m]][k]) / comp.members.length;
+                    }
+                    shift = [-Math.floor(mean[0] + 1e-6), -Math.floor(mean[1] + 1e-6), -Math.floor(mean[2] + 1e-6)];
+                    for (ix = 0; ix < opt.nx; ix++) for (iy = 0; iy < opt.ny; iy++) for (iz = 0; iz < opt.nz; iz++) {
+                        for (m = 0; m < comp.members.length; m++) {
+                            at = list[comp.members[m]];
+                            var tt = mol.T[comp.members[m]];
+                            emit(at, [at.g[0] + tt[0] + shift[0] + ix, at.g[1] + tt[1] + shift[1] + iy, at.g[2] + tt[2] + shift[2] + iz]);
+                        }
                     }
                 }
             }
+            else {
+                for (m = 0; m < list.length; m++) {
+                    at = list[m];
+                    images = coreLatticeImages(at.g, opt.nx, opt.ny, opt.nz, opt.boundary);
+                    for (im = 0; im < images.length; im++) emit(at, images[im]);
+                }
+            }
             out.push('#');
             return out.join('\n') + '\n';
         }
@@ -3018,7 +3140,7 @@ var CIFTools;
                 // This approach to binary parsing wastes a bit of memory to trade for speed compared to:
                 //
                 //   let value = buffer.subarray(offset, offset + length); //new Uint8Array(buffer.buffer, offset, length);
-                // 
+                //
                 // It turns out that using the view created by subarray probably uses DataView
                 // in the background, which causes the element access to be several times slower
                 // than creating the new byte array.
@@ -4342,7 +4464,7 @@ var CIFTools;
                     if (index === void 0) {
                         // increment the length
                         accLength += s.length;
-                        // store the string and index                   
+                        // store the string and index
                         index = strings.length;
                         strings[index] = s;
                         map[s] = index;
@@ -55403,7 +55525,7 @@ class UtilsCls {
     }
 
     //Convert a three-letter residue name to a one-letter residue abbreviation, e.g., 'LYS' to 'K', or ' A' to 'A' for nucleotides.
-    residueName2Abbr(residueName) { this.icn3dui;
+    residueName2Abbr(residueName, bOneLetter) { this.icn3dui;
       let pos = residueName.indexOf(' ');
       if(pos > 0) {
           residueName = residueName.substr(0, pos);
@@ -55498,7 +55620,12 @@ class UtilsCls {
           return 'O';
 
         default:
-          return residueName.trim();
+          if(bOneLetter) {
+            return 'X';
+          }
+          else {
+            return residueName.trim();
+          }
       }
     }
 
@@ -55574,15 +55701,20 @@ class UtilsCls {
     }
 
     getIdArray(resid) { this.icn3dui;
-        //var idArray = resid.split('_');
         let idArray = [];
 
         if(resid) {
-            let pos1 = resid.indexOf('_');
-            let pos2 = resid.lastIndexOf('_');
-            idArray.push(resid.substr(0, pos1));
-            idArray.push(resid.substr(pos1 + 1, pos2 - pos1 - 1));
-            idArray.push(resid.substr(pos2 + 1));
+          let itemArray = resid.split('_');
+
+          if(resid.indexOf('pdb_') == 0 ) { // e.g., pdb_00001GPK_A_15
+            idArray.push(itemArray[0] + '_' + itemArray[1]);
+            for(let i = 2, il = itemArray.length; i < il; ++i) {
+              idArray.push(itemArray[i]);
+            }
+          }
+          else {
+            idArray = itemArray;
+          }
         }
 
         return idArray;
@@ -55593,12 +55725,12 @@ class UtilsCls {
       let bArray = b.split(',');
       let aIdArray, bIdArray;
       if(type == 'save1') {
-        aIdArray = me.utilsCls.getIdArray(aArray[0]); //aArray[0].split('_');
-        bIdArray = me.utilsCls.getIdArray(bArray[0]); //bArray[0].split('_');
+        aIdArray = me.utilsCls.getIdArray(aArray[0]); 
+        bIdArray = me.utilsCls.getIdArray(bArray[0]); 
       }
       else if(type == 'save2') {
-        aIdArray = me.utilsCls.getIdArray(aArray[1]); //aArray[1].split('_');
-        bIdArray = me.utilsCls.getIdArray(bArray[1]); //bArray[1].split('_');
+        aIdArray = me.utilsCls.getIdArray(aArray[1]); 
+        bIdArray = me.utilsCls.getIdArray(bArray[1]); 
       }
       let aChainid = aIdArray[0] + '_' + aIdArray[1];
       let bChainid = bIdArray[0] + '_' + bIdArray[1];
@@ -57513,6 +57645,9 @@ class ClickMenu {
         me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_mmcifid', 'Please input mmCIF ID');
         });
+        me.myEventCls.onIds("#" + me.pre + "mn1_codid", "click", function(e) { me.icn3d; //e.preventDefault();
+           me.htmlCls.dialogCls.openDlg('dl_codid', 'Please input COD ID');
+        });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_mmdbid', 'Please input MMDB or PDB ID');
@@ -58052,7 +58187,7 @@ class ClickMenu {
                        thisClass.setLogCmd("link to compounds with structure similar to CID " + ic.inputid + ": " + url, false);
                }
                else {
-                   let idArray = ic.inputid.split('_');
+                   let idArray = me.utilsCls.getIdArray(ic.inputid);
                    
                    if(idArray.length === 1) {
                        url = me.htmlCls.baseUrl + "vastplus/vastplus.cgi?uid=" + ic.inputid;
@@ -59114,17 +59249,14 @@ class ClickMenu {
 
     }
 
-    async setSupercell(n) { let me = this.icn3dui, ic = me.icn3d;
-      ic.loadCIFCls.loadCIF(ic.cifData, undefined, ic.cifText, false, n);
-
-      if(Object.keys(ic.proteins).length == 0 || Object.keys(ic.nucleotides).length == 0) {
-        ic.pk = 1;
-        ic.opts['pk'] = 'atom';
+    setSupercell(n) { let me = this.icn3dui, ic = me.icn3d;
+      if(ic.cifData) {
+         ic.loadCIFCls.loadCIF(ic.cifData, undefined, ic.cifText, false, n);
+         
+         ic.setStyleCls.setAtomStyleByOptions(ic.opts);
+         ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+         ic.drawCls.draw();
       }
-      
-      ic.setStyleCls.setAtomStyleByOptions(ic.opts);
-      ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
-      await ic.ParserUtilsCls.renderStructure();
     }
 
     clickMenu6() { let me = this.icn3dui, ic = me.icn3d;
@@ -59144,20 +59276,20 @@ class ClickMenu {
            ic.drawCls.draw();
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mn6_assembly0", "click", async function(e) { me.icn3d; //e.preventDefault();
-           await thisClass.setSupercell(0);
+        me.myEventCls.onIds("#" + me.pre + "mn6_assembly0", "click", function(e) { me.icn3d; //e.preventDefault();
+           thisClass.setSupercell(0);
            thisClass.setLogCmd('set supercell 0', true);
         });
-        me.myEventCls.onIds("#" + me.pre + "mn6_assembly1", "click", async function(e) { me.icn3d; //e.preventDefault();
-           await thisClass.setSupercell(1);
+        me.myEventCls.onIds("#" + me.pre + "mn6_assembly1", "click", function(e) { me.icn3d; //e.preventDefault();
+           thisClass.setSupercell(1);
            thisClass.setLogCmd('set supercell 1', true);
         });
-        me.myEventCls.onIds("#" + me.pre + "mn6_assembly2", "click", async function(e) { me.icn3d; //e.preventDefault();
-           await thisClass.setSupercell(2);
+        me.myEventCls.onIds("#" + me.pre + "mn6_assembly2", "click", function(e) { me.icn3d; //e.preventDefault();
+           thisClass.setSupercell(2);
            thisClass.setLogCmd('set supercell 2', true);
         });
-        me.myEventCls.onIds("#" + me.pre + "mn6_assembly3", "click", async function(e) { me.icn3d; //e.preventDefault();
-           await thisClass.setSupercell(3);
+        me.myEventCls.onIds("#" + me.pre + "mn6_assembly3", "click", function(e) { me.icn3d; //e.preventDefault();
+           thisClass.setSupercell(3);
            thisClass.setLogCmd('set supercell 3', true);
         });
 
@@ -60515,6 +60647,7 @@ class SetMenu {
         html += this.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
         html += this.getLink('mn1_mmcifid', 'RCSB mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
         //html += this.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
+//        html += this.getLink('mn1_codid', 'COD ID ' + me.htmlCls.wifiStr, 1, 2);
 
         html += this.getLink('mn1_cid', 'PubChem CID/Name/InChI ' + me.htmlCls.wifiStr, 1, 2);
         html += this.getLink('mn1_smiles', 'Chemical SMILES ', undefined, 2);
@@ -60569,7 +60702,7 @@ class SetMenu {
         //html += this.getMenuText('mn1_fold', 'AlphaFold/ESM', undefined, undefined, 1);
         html += this.getMenuText('mn1_fold', 'Predict by Seq.', undefined, undefined, 1);
         html += "<ul>";
-        html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
+        //html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
         //html += this.getMenuUrl('mn1_esmfold_link', "https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb", "ESMFold via ColabFold" + me.htmlCls.wifiStr, undefined, 2);
         html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold' + me.htmlCls.wifiStr, undefined, 2);
         html += "</ul>";
@@ -61755,16 +61888,17 @@ class SetMenu {
 
             html += this.getLink('mn6_DSSP', 'DSSP Secondary', undefined, 1);
 
-            let bInputid = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.bcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.mmdbafid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
+            let bInputid = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.bcifid !== undefined  || me.cfg.mmtfid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.mmdbafid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
 
             //if(bInputid) {
               html += this.getMenuText('assemblyWrapper', 'Assembly', undefined, 1, 1);
               html += "<ul>";
 
-              if(!bInputid || me.cfg.mmcifid !== undefined || me.cfg.bcifid !== undefined) { // e.g., cif file input
-                html += this.getRadio('mn6_assembly', 'mn6_assembly0', 'Original Assembly', undefined, 1, 2);
+              if(!bInputid || me.cfg.mmcifid !== undefined || me.cfg.bcifid !== undefined || me.cfg.mmtfid !== undefined) { // e.g., cif file input
+                html += this.getRadio('mn6_assembly', 'mn6_assembly0', 'Biological Assembly', undefined, 1, 2);
+                html += this.getRadio('mn6_assembly', 'mn6_assemblyNo', 'Asymmetric Unit', undefined, 1, 2);
                 html += this.getRadio('mn6_assembly', 'mn6_assembly1', '1 x 1 x 1', true, 1, 2);
-                html += this.getRadio('mn6_assembly', 'mn6_assembly2', '2 x 2 x 2', undefined, 1, 2);
+                html += this.getRadio('mn6_assembly', 'mn6_assembly2', '2 x 2 x 2', undefined, undefined, 2);
                 html += this.getRadio('mn6_assembly', 'mn6_assembly3', '3 x 3 x 3', undefined, 1, 2);
               }
               else if(!me.cfg.bu) {
@@ -62173,7 +62307,6 @@ class Dialog {
                       if(status.bSetsInit2) thisClass.openDlg2Ddgm(me.pre + 'dl_definedsets');
                   }
                   else {
-                      //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                       ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
                   }
               }
@@ -62262,7 +62395,6 @@ class Dialog {
               let status = thisClass.getDialogStatus().status;
 
               if((!status.bSelectannotationsInit2) &&(!status.bGraph2) &&(!status.bLineGraph2) &&(!status.bScatterplot2) &&(!status.bHbondplot2) &&(!status.bLigplot2) &&(!status.bTable2) &&(!status.bAlignmentInit2) ) {
-                    //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                     ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
               }
           },
@@ -62307,8 +62439,7 @@ class Dialog {
                 }
             }
             else {
-                //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH,(me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT) * 0.5, true);
-                ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH,(me.htmlCls.HEIGHT) * 0.5, true);
+                //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH,(me.htmlCls.HEIGHT) * 0.5, true);
 
                 //height =(me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT) * 0.5;
                 height =(me.htmlCls.HEIGHT) * 0.5;
@@ -62348,7 +62479,6 @@ class Dialog {
                               if(status.bSetsInit2) thisClass.openDlg2Ddgm(me.pre + 'dl_definedsets');
                           }
                           else {
-                              //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                               ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
                           }
                       }
@@ -63020,6 +63150,12 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_mmcif'>Load</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_codid' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_codid', 'Please input a COD ID');
+        html += "COD ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "codid' value='1000041' size=8> ";
+        html += me.htmlCls.buttonStr + "reload_cod'>Load</button>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_mmdbid' class='" + dialogClass + "' style='max-width:500px'>";
         html += this.addNotebookTitle('dl_mmdbid', 'Please input an MMDB ID');
         html += "MMDB or PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbid' value='1TUP' size=8> <br><br>";
@@ -64475,7 +64611,20 @@ class Events {
         let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
 
         if(nameArray.length == 0) {
-            nameArray = $("#" + me.pre + "atomsCustom").val();
+            // nameArray = $("#" + me.pre + "atomsCustom").val();
+            
+            // choose the first chain for each structure
+            nameArray = [];
+            let structureHash = {};
+            let chains = ic.resid2specCls.atoms2chains(ic.hAtoms);
+
+            for(let chainid in chains) {
+                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
+                if(!structureHash.hasOwnProperty(atom.structure) && (ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial))) {
+                    nameArray.push(chainid);
+                    structureHash[atom.structure] = 1;
+                }
+            }
         }
 
         if(nameArray.length > 0) {
@@ -64495,20 +64644,6 @@ class Events {
         }
 
         if(bMsa) {
-            // choose the first chain for each structure
-            if(nameArray.length == 0) {
-                nameArray = [];
-                let structureHash = {};
-                
-                for(let chainid in ic.chains) {
-                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
-                    if(!structureHash.hasOwnProperty(atom.structure) && (ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial))) {
-                        nameArray.push(chainid);
-                        structureHash[atom.structure] = 1;
-                    }
-                }
-            }
-
             await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
         }
         else {
@@ -64682,7 +64817,7 @@ class Events {
         let idArray = ids.split(',');
 
         if(!bAppend) {
-            if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
+            if(idArray.length == 1 && (idArray[0].length == 4 || idArray[0].indexOf('pdb_') == 0 || !isNaN(idArray[0])) ) {
                 thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
                 let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
                 window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
@@ -64694,8 +64829,8 @@ class Events {
             }
         }
         else {
-            // single MMDB ID could show memebranes
-            if(!ic.structures && idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
+            // single MMDB ID could show membranes
+            if(!ic.structures && idArray.length == 1 && (idArray[0].length == 4 || idArray[0].indexOf('pdb_') == 0 || !isNaN(idArray[0])) ) {
                 thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
                 let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
                 window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
@@ -65183,7 +65318,7 @@ class Events {
                if(!me.cfg.notebook) dialog.dialog( "close" );
                thisClass.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
-               window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
+               window.open(hostUrl + '?bcifid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
            }
         });
 
@@ -65527,7 +65662,7 @@ class Events {
                 await ic.scapCls.retrieveScap(snp, bInteraction);
                 thisClass.setLogCmd('scap interaction ' + snp, true);
 
-                let idArray = snp.split('_'); //stru_chain_resi_snp
+                let idArray = me.utilsCls.getIdArray(snp); //stru_chain_resi_snp
                 let select = '.' + idArray[1] + ':' + idArray[2];
                 let name = 'snp_' + idArray[1] + '_' + idArray[2];
                 thisClass.setLogCmd("select " + select + " | name " + name, true);
@@ -65566,7 +65701,6 @@ class Events {
            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
            window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
         });
-
         me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
@@ -65577,6 +65711,23 @@ class Events {
            }
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_cod", "click", function(e) { let ic = me.icn3d;
+           e.preventDefault();
+           if(!me.cfg.notebook) dialog.dialog( "close" );
+           thisClass.setLogCmd("load cod " + $("#" + me.pre + "codid").val(), false);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?codid=' + $("#" + me.pre + "codid").val(), urlTarget);
+        });
+        me.myEventCls.onIds("#" + me.pre + "codid", "keyup", function(e) { let ic = me.icn3d;
+           if (e.keyCode === 13) {
+               e.preventDefault();
+               if(!me.cfg.notebook) dialog.dialog( "close" );
+               thisClass.setLogCmd("load cod " + $("#" + me.pre + "codid").val(), false);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?codid=' + $("#" + me.pre + "codid").val(), urlTarget);
+           }
+        });
+
 
         me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
@@ -68162,7 +68313,7 @@ class Events {
             await ic.scapCls.retrieveScap(snp, bInteraction);
             thisClass.setLogCmd('scap interaction ' + snp, true);
 
-            let idArray = snp.split('_'); //stru_chain_resi_snp
+            let idArray = me.utilsCls.getIdArray(snp); //stru_chain_resi_snp
             let select = '.' + idArray[1] + ':' + idArray[2];
             let name = 'snp_' + idArray[1] + '_' + idArray[2];
             thisClass.setLogCmd("select " + select + " | name " + name, true);
@@ -78186,6 +78337,43 @@ class Camera {
     //    }
     }
 
+    // Keep the slab plane at the same position relative to the molecule when zooming.
+    // In perspective mode zooming moves the camera along the view direction, so the near plane
+    // (distance from the camera) has to move with it. In orthographic mode zooming only changes
+    // the frustum size and the camera does not move, so the slab plane already stays fixed.
+    updateSlabByZoom() { let ic = this.icn3d, me = ic.icn3dui;
+        if(ic.opts['slab'] !== 'yes' || me.bNode) return;
+        if(ic.opts.camera.toLowerCase() !== 'perspective') return;
+
+        let bInstance = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > ic.maxatomcnt) ? true : false;
+        if(bInstance) return; // near plane is fixed at 0.1 for instancing
+
+        let cam = (ic.bControlGl) ? window.cam : ic.cam;
+        let controls = (ic.bControlGl) ? window.controls : ic.controls;
+ 
+        // at zoom = 1 the slab plane is ic.maxD * camMaxDFactor from the camera, i.e. the plane through
+        // the center (or 10 angstroms in front of it when fog is on to keep some surrounding residues)
+        let offset = (ic.camMaxDFactorFog !== undefined) ? 10 : 0;
+
+        // current distance from the camera to the center of rotation, which changes with zooming
+        let dist = cam.position.distanceTo(controls.target);
+
+        // keep the plane at the same position relative to the molecule
+        let nearClip = Math.max(0.1, dist - offset);
+
+        if(Math.abs(cam.near - nearClip) > 1e-6) {
+            cam.near = nearClip;
+            cam.updateProjectionMatrix();
+            if(ic.cam && ic.cam !== cam) {
+                ic.cam.near = nearClip;
+                ic.cam.updateProjectionMatrix();
+            }
+        }
+
+        // the impostor shaders (spheres, cylinders) clip with the nearClip uniform
+        if(ic.uniforms && ic.uniforms.nearClip) ic.uniforms.nearClip.value = nearClip;
+    }
+
     setSlab() { let ic = this.icn3d, me = ic.icn3dui;
         if(ic.bControlGl && !me.bNode) {
             let maxD = ic.maxD;
@@ -78301,7 +78489,8 @@ class Fog {
                 else {
                     // adjust
                     let zoomFactor = (ic._zoomFactor > 1) ? ic._zoomFactor * 1.0 : ic._zoomFactor;
-                    ic.scene.fog = new Fog$1(background, 2.5 * ic.maxD * zoomFactor, 4 * ic.maxD * zoomFactor);
+                    let fogStrength = 2; // 1 = current, >1 = stronger
+                    ic.scene.fog = new Fog$1(background, (3 - 0.5 / fogStrength) * ic.maxD * zoomFactor, (3 + 1.0 / fogStrength) * ic.maxD * zoomFactor);
                     ic.bSetFog = true;
                     ic.camMaxDFactorFog = 3;
                 }
@@ -80526,6 +80715,8 @@ class Tube {
 
         let prevAxis1 = new Vector3$1(), prevAxis2;
         for (let i = 0, lim = pnts.length; i < lim; ++i) {
+            if(!pnts[i]) continue;
+            
             let r, idx = (i - 1) * axisDivInv;
 
             if (i === 0) {
@@ -80558,7 +80749,7 @@ class Tube {
             }
 
             let delta, axis1, axis2;
-            if (i < lim - 1) {
+            if (i < lim - 1 && pnts[i + 1]) {
                 delta = pnts[i].clone().sub(pnts[i + 1]);
                 axis1 = new Vector3$1(0, -delta.z, delta.y).normalize().multiplyScalar(r);
                 axis2 = delta.clone().cross(axis1).normalize().multiplyScalar(r);
@@ -84544,7 +84735,6 @@ class Surface {
             let chainStr = (Object.keys(chainHash).length > 1) ? '<th>Chain</th>' : '';
             html += '<tr>' + structureStr + chainStr + '<th>Residue</th><th>Number</th><th>SASA (&#8491;<sup>2</sup>)</th><th>Percent Out</th><th>In/Out</th></tr>';
             for(let resid in ic.resid2area) {
-                //var idArray = resid.split('_');
                 let pos = resid.lastIndexOf('_');
                 let resn = resid.substr(pos + 1);
 
@@ -85198,6 +85388,8 @@ class ApplyClbonds {
                     // only apply to displayed atoms
                     // if(!ic.dAtoms.hasOwnProperty(line.serial1) || !ic.dAtoms.hasOwnProperty(line.serial2)) continue;
 
+                    if(!ic.atoms[line.serial1] || !ic.atoms[line.serial2]) continue;
+
                     line.position1 = ic.atoms[line.serial1].coord;
                     line.position2 = ic.atoms[line.serial2].coord;
 
@@ -85328,6 +85520,7 @@ class ApplyClbonds {
                         if(type == 'chemical') continue; // just connect checmicals together
 
                         if(ic.clbondpnts[atom0.structure] === undefined) ic.clbondpnts[atom0.structure] = [];
+                        if(ic.clbondpnts[atom1.structure] === undefined) ic.clbondpnts[atom1.structure] = [];
                         ic.clbondpnts[atom0.structure].push(resid0);
                         ic.clbondpnts[atom1.structure].push(resid1);
 
@@ -85873,9 +86066,9 @@ class ApplyOther {
                 }
             }
 
-            ic.lineCls.createLines(ic.lines);
-            if(!ic.planes) ic.planes = [];
-            ic.cylinderCls.createPlanes(ic.planes);
+            // ic.lineCls.createLines(ic.lines);
+            // if(!ic.planes) ic.planes = [];
+            // ic.cylinderCls.createPlanes(ic.planes);
     //    }
 
         // distance sets
@@ -85998,6 +86191,10 @@ class ApplyOther {
                 ic.pk = 3;
                 break;
         }
+
+        ic.lineCls.createLines(ic.lines);
+        if(!ic.planes) ic.planes = [];
+        ic.cylinderCls.createPlanes(ic.planes);
     }
 
     applyChemicalbindingOptions(options) { let ic = this.icn3d, me = ic.icn3dui;
@@ -87144,6 +87341,8 @@ class Impostor {
 
         let shiness = ic.shininess / 100.0 * 0.5;
 
+        let fogRGB = background.clone().convertLinearToSRGB();
+
         ic.uniforms = UniformsUtils.merge([
           UniformsLib.common,
           {
@@ -87164,7 +87363,8 @@ class Impostor {
             nearClip: { type: "f", value: nearClip },
             ortho: { type: "f", value: 0.0 },
             shrink: { type: "f", value: 0.13 },
-            fogColor: { type: "v3", value: [background.r, background.g, background.b] },
+            //fogColor: { type: "v3", value: [background.r, background.g, background.b] },
+            fogColor: { type: "v3", value: [fogRGB.r, fogRGB.g, fogRGB.b] },
             fogNear: { type: "f", value: near },
             fogFar: { type: "f", value: far },
             fogDensity: { type: "f", value: 2.0 }
@@ -105397,6 +105597,9 @@ class WebGLPathTracer {
 
         cam = this.setDirectLight(cam);
 
+        // move the slab plane according to the zoom
+	    if(ic.opts['slab'] === 'yes') ic.cameraCls.updateSlabByZoom();
+
         if(!ic.bVr) ic.renderer.setPixelRatio( window.devicePixelRatio ); // r71
 
         if(ic.bVr) {
@@ -108960,7 +109163,7 @@ class AnnoCddSite {
         ic.bAjaxCddSite = true;
     }
 
-    getResiArrayStr(resiNCBIArray, chainid) { let ic = this.icn3d; ic.icn3dui;
+    getResiArrayStr(resiNCBIArray, chainid) { let ic = this.icn3d, me = ic.icn3dui;
         let resiArrayStr = '';
         for(let i = 0, il = resiNCBIArray.length; i < il; ++i) {
             let resiNCBI = resiNCBIArray[i] + 1; // zero-based
@@ -108968,7 +109171,8 @@ class AnnoCddSite {
             let resid = ic.ncbi2resid[residNCBI];
             if(!resid) resid = residNCBI; // this happens sometimes, e.g., Q9Y4K1
 
-            let resi = resid.split('_')[2];
+            let idArray = me.utilsCls.getIdArray(resid);
+            let resi = idArray[2];
             if(i > 0) resiArrayStr += ',';
             resiArrayStr += resi;
         }
@@ -110064,7 +110268,8 @@ class AnnoIg {
                 let residArray = Object.keys(residHash);
 
                 // delete the following loops
-                let lastPos = ic.setSeqAlignCls.getPosFromResi(chnid, residArray[residArray.length - 1].split('_')[2]);
+                let idArray = me.utilsCls.getIdArray(residArray[residArray.length - 1]);
+                let lastPos = ic.setSeqAlignCls.getPosFromResi(chnid, idArray[2]);
 
                 for(let j = lastPos + 1, jl = ic.chainsSeq[chnid].length; j < jl; ++j) {
                     let resi = ic.chainsSeq[chnid][j].resi;
@@ -110080,7 +110285,8 @@ class AnnoIg {
                 }
 
                 // delete the previous loops
-                ic.setSeqAlignCls.getPosFromResi(chnid, residArray[0].split('_')[2]);
+                idArray = me.utilsCls.getIdArray(residArray[0]);
+                ic.setSeqAlignCls.getPosFromResi(chnid, idArray[2]);
 
                 for(let j = lastPos - 1; j >= 0; --j) {
                     let resi = ic.chainsSeq[chnid][j].resi;
@@ -111083,8 +111289,9 @@ class AnnoSnpClinVar {
         let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.chains[chnid]);
         // for(let i = 1, il = ic.giSeq[chnid].length; i <= il; ++i) {
         for(let resid in residHash) {
-            let i = resid.split('_')[2];
-            
+            let idArray = me.utilsCls.getIdArray(resid);
+            let i = idArray[2];
+
             if(resi2index[i] !== undefined) {            
                 ++snpCnt;
                 let allDiseaseTitle = '';
@@ -113277,7 +113484,6 @@ class Domain3d {
 			// if(fromPos >= start && toPos <= end) {
 				if(ssCnt > 0) jsonStr += ', ';
 				jsonStr += '[' + sstype + ',' + fromPos + ',' + toPos + ',' + substruct[k].x1.toFixed(2) + ',' + substruct[k].y1.toFixed(2) + ',';
-				// jsonStr += '[' + sstype + ',' + residFrom.split('_')[2] + ',' + residTo.split('_')[2] + ',' + substruct[k].x1.toFixed(2) + ',' + substruct[k].y1.toFixed(2) + ',';
 				jsonStr += substruct[k].z1.toFixed(2) + ',' + substruct[k].x2.toFixed(2) + ',' + substruct[k].y2.toFixed(2) + ',' + substruct[k].z2.toFixed(2) + ']';
 				++ssCnt;
 			// }
@@ -113294,7 +113500,6 @@ class Domain3d {
 		for(let j = startAll; j <= endAll; ++j) {
 			let ncbiResid = chnid + '_' + j;
 			let resid = ic.ncbi2resid[ncbiResid];
-			resid.split('_')[2];
 
 			let pos = j;
 
@@ -113302,7 +113507,6 @@ class Domain3d {
 
 			if(!residueHash.hasOwnProperty(resid)) {
 				jsonStr += '[' + pos + ',' + 0 + ',' + fakeCoord + ',' + fakeCoord + ',' + fakeCoord + ']';
-				// jsonStr += '[' + resi + ',' + 0 + ',' + fakeCoord + ',' + fakeCoord + ',' + fakeCoord + ']';
 			}
 			else {
 				let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
@@ -113311,7 +113515,6 @@ class Domain3d {
 				let restype = (me.parasCls.resn2restype[atom.resn]) ? me.parasCls.resn2restype[atom.resn] : 0;
 				
 				jsonStr += '[' + pos + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' + atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
-				// jsonStr += '[' + resi + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' + atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
 			}
 
 			++domainCnt;		
@@ -119149,7 +119352,6 @@ class GetGraph {
           for(let i = 0, il = graphJson.nodes.length; i < il; ++i) {
               let node = graphJson.nodes[i];
               //node.r: 1_1_1KQ2_A_1
-              //var idArray = node.r.split('_');
               let idArray = [];
               idArray.push('');
               idArray.push('');
@@ -119328,8 +119530,8 @@ class GetGraph {
     compNode(a, b, bReverseChain) { let ic = this.icn3d, me = ic.icn3dui;
       let resid1 = a.r.substr(4); // 1_1_1KQ2_A_1
       let resid2 = b.r.substr(4); // 1_1_1KQ2_A_1
-      let aIdArray = me.utilsCls.getIdArray(resid1); //resid1.split('_');
-      let bIdArray = me.utilsCls.getIdArray(resid2); //resid2.split('_');
+      let aIdArray = me.utilsCls.getIdArray(resid1);
+      let bIdArray = me.utilsCls.getIdArray(resid2);
       let aChainid = aIdArray[0] + '_' + aIdArray[1];
       let bChainid = bIdArray[0] + '_' + bIdArray[1];
       let aResi = parseInt(aIdArray[2]);
@@ -120382,7 +120584,7 @@ class ViewInterPairs {
             residname2 =(type == 'save1') ? residname1_residname2[1] : residname1_residname2[0];
 
             // stru_chain_resi_resn
-            let ids = residname1.split('_');
+            let ids = me.utilsCls.getIdArray(residname1);
             if(i > 0 && residname1 != prevResidname1) {
                 bondCnt.push({res1: prevResidname1, res2: residname2List, cntHbond: cntHbond, cntIonic: cntIonic, cntContact: cntContact, cntHalegen: cntHalegen, cntPication: cntPication, cntPistacking: cntPistacking});
 
@@ -121783,8 +121985,8 @@ class AlignParser {
                     //var scale = data2.transform.scale / factor;
                     let tMaster = data2.transform.translate.master;
                     let tMVector = new Vector3$1(tMaster[0] / factor, tMaster[1] / factor, tMaster[2] / factor);
-                    let tSlave = data2.transform.translate.slave;
-                    let tSVector = new Vector3$1(tSlave[0] / factor, tSlave[1] / factor, tSlave[2] / factor);
+                    let tQuery = data2.transform.translate.slave; // actually means query protein
+                    let tSVector = new Vector3$1(tQuery[0] / factor, tQuery[1] / factor, tQuery[2] / factor);
                     let rotation = data2.transform.rotate;
                     let rMatrix = [];
                     for(let i = 0, il = rotation.length; i < il; ++i) { // 9 elements
@@ -122028,44 +122230,6 @@ class ChainalignParser {
             // calculate secondary structures with applyCommandDssp
             //$.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 await ic.pdbParserCls.applyCommandDssp(true);
-//!!!
-/*
-                // original version =============
-                // align PDB chains
-                for(let index in ic.pdbChainIndexHash) {
-                    //ic.pdbChainIndexHash[index] = mmdbid_q_tmp + "_" + ic.chain_q + "_" + ic.mmdbid_t + "_" + ic.chain_t;
-                    let idArray = ic.pdbChainIndexHash[index].split('_');
-                    mmdbid_q = idArray[0];
-                    let chain_q = idArray[1];
-                    mmdbid_t = idArray[2];
-                    let chain_t = idArray[3];
-
-                    thisClass.transformStructure(mmdbid_q, index-1, 'query');                
-                }
-
-                // dynamically align pairs in ic.afChainIndexHash
-                let ajaxArray = [], indexArray = [], struArray = [];
-                let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
-                let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
-
-                let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).split(' | ') : [];
-
-                for(let index in ic.afChainIndexHash) {
-                    let idArray = ic.afChainIndexHash[index].split('_');
-                    mmdbid_q = idArray[0];
-                    let chain_q = idArray[1];
-                    let chainid_q = mmdbid_q + '_' + chain_q;
-
-                    mmdbid_t = idArray[2];
-                    let chain_t = idArray[3];
-                    let chainid_t = mmdbid_t + '_' + chain_t;
-
-                    // let atomSet_t = (resRangeArray[0]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainid_t, true).hAtoms : ic.chains[chainid_t];
-                    // let atomSet_q = (resRangeArray[index]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainid_q, true).hAtoms : ic.chains[chainid_q];
-                    let atomSet_t = (resRangeArray[0]) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainid_t, true).hAtoms : ic.chains[chainid_t];
-                    let atomSet_q = (resRangeArray[index]) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainid_q, true).hAtoms : ic.chains[chainid_q];
-                // end of original version =============
-*/                
 
                 // new version to be done for VASTsrv ==============
                 // dynamically align pairs in all chainids
@@ -122534,10 +122698,10 @@ class ChainalignParser {
         return chainidArray;
     }
 
-    addPostfixForStructureids(structArray) { let ic = this.icn3d; ic.icn3dui;
+    addPostfixForStructureids(structArray) { let ic = this.icn3d, me = ic.icn3dui;
         let struct2cnt = {};
         for(let i = 0, il = structArray.length; i < il; ++i) {
-            if(structArray[i].toLowerCase().toLowerCase().substr(0,8) == 'pdb_0000') structArray[i] = structArray[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
+            if((me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined) && structArray[i].toLowerCase().toLowerCase().substr(0,8) == 'pdb_0000') structArray[i] = structArray[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
 
             let struct = structArray[i].toUpperCase(); 
 
@@ -122561,6 +122725,8 @@ class ChainalignParser {
 
         ic.opts['proteins'] = 'c alpha trace';
 
+        if(!chainalign) return;
+        
         let alignArray = chainalign.split(',');
         let domainArray = (me.cfg.domainids) ? me.cfg.domainids.split(',') : [];
         if(domainArray.length < alignArray.length) domainArray = [];
@@ -122633,7 +122799,7 @@ class ChainalignParser {
                 let domainalign = (domainArray.length > 0) ? domainArray[index] + "," + domainArray[0] : undefined;
 
                 // TM-align (me.cfg.aligntool == 'tmalign') needs to input PDB
-                if(me.cfg.aligntool != 'tmalign' && ic.mmdbid_t.length == 4 && ic.mmdbid_q.length == 4) {
+                if(me.cfg.aligntool != 'tmalign' && (ic.mmdbid_t.length == 4 || ic.mmdbid_t.indexOf('pdb_') == 0) && (ic.mmdbid_q.length == 4 || ic.mmdbid_q.indexOf('pdb_') == 0)) {
                     let urlalign;
                     
                     if(domainArray.length > 0) {
@@ -122922,7 +123088,7 @@ class ChainalignParser {
         }
         else {
             for(let i = 0, il = structArrayTmp.length; i < il; ++i) {
-                if(structArrayTmp[i].toLowerCase().substr(0,8) == 'pdb_0000') structArrayTmp[i] = structArrayTmp[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
+                if((me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined) && structArrayTmp[i].toLowerCase().substr(0,8) == 'pdb_0000') structArrayTmp[i] = structArrayTmp[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
 
                 let id = structArrayTmp[i].toUpperCase();
                 if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
@@ -124453,6 +124619,19 @@ class MmcifParser {
         await ic.opmParserCls.loadOpmData(data, mmcifid, undefined, 'mmcif', undefined, bText);
     }
 
+    async downloadCod(codid) { let ic = this.icn3d, me = ic.icn3dui;
+        //ic.bCid = undefined;
+
+        ic.ParserUtilsCls.setYourNote(codid.toUpperCase() + '(COD) in iCn3D');
+
+        let url = "https://www.crystallography.net/cod/" + codid + ".cif";
+        // let url = "https://www.crystallography.net/cif/1/00/00/1000041.cif";
+        let data = await me.getAjaxPromise(url, 'text', true);
+
+        let bText = true;
+        ic.loadCIFCls.loadCIF(data, codid, bText);
+    }
+
     async downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d, me = ic.icn3dui;
       try {
         // let url = "https://files.rcsb.org/download/" + mmcifid + ".cif";
@@ -124566,6 +124745,11 @@ class MmcifParser {
             ic.opts['color'] = 'structure';
         }
 
+        if(Object.keys(ic.proteins).length == 0 || Object.keys(ic.nucleotides).length == 0) {
+            ic.pk = 1;
+            ic.opts['pk'] = 'atom';
+        }
+
         ic.opmParserCls.modifyUIMapAssembly();
 
         await ic.pdbParserCls.addSecondary(bAppend);
@@ -124659,9 +124843,10 @@ class MmdbParser {
         me.cfg.query_id = idArray[0];
         me.cfg.blast_rep_id = idArray[1];
 
-        let mmdbid = me.cfg.blast_rep_id.split('_')[0]; // 1TSR_A, XP_003256700.1, Q9H3D4.1
+        let textArray = me.utilsCls.getIdArray(me.cfg.blast_rep_id);
+        let mmdbid = textArray[0]; // 1TSR_A, XP_003256700.1, Q9H3D4.1
 
-        if(mmdbid.length == 4) { // pdb
+        if(mmdbid.length == 4 || mmdbid.indexOf('pdb_') == 0) { // pdb
             await this.downloadMmdb(mmdbid);
         }
         else {
@@ -124813,7 +124998,7 @@ class MmdbParser {
                 if(ic.chainid2sid[chainid] == me.cfg.ligand.substr(3)) {
                     // save a set named me.cfg.ligand
                     let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.chains[chainid]);
-                    let idArray = Object.keys(residueHash)[0].split('_');
+                    let idArray = me.utilsCls.getIdArray(Object.keys(residueHash)[0]);
                     let select = '.' + idArray[1] + ':' + idArray[2];
 
                     await ic.selByCommCls.selectByCommand(select, me.cfg.ligand, me.cfg.ligand);
@@ -124949,8 +125134,8 @@ class MmdbParser {
 
         if(type === undefined || type === 'target') {
             // if a command contains "load...", the commands should not be cleared with init()
-            let bKeepCmd = (ic.bCommandLoad) ? true : false;
-            if(!ic.bStatefile) ic.init(bKeepCmd);
+            let bClearCmd = (ic.bCommandLoad) ? false : true;
+            if(!ic.bStatefile) ic.init(bClearCmd);
 
             ic.chainsColor = {};
             ic.chainsGene = {};
@@ -125190,7 +125375,7 @@ class BcifParser {
 
         if (parsed.isError) {
             // report error:
-            var aaa = 1; //alert("The Binary CIF data can NOT be parsed: " + parsed.toString());
+            var aaa = 1; //alert("1 The Binary CIF data can NOT be parsed: " + parsed.toString());
             return;
         }
 
@@ -126155,7 +126340,8 @@ class OpmParser {
             if(!pdbid) pdbid = ic.defaultPdbId;
 
             //if(me.cfg.mmtfid === undefined && me.cfg.bcifid === undefined) { // skip opm for bcif files
-                let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
+                let shortPdbid = pdbid.indexOf('pdb_0000') == 0 ? pdbid.substr(8) : pdbid;
+                let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + shortPdbid.toLowerCase();
 
                 let opmdata = await me.getAjaxPromise(url, 'jsonp', false);
         
@@ -126417,8 +126603,8 @@ class PdbParser {
     async loadPdbData(data, pdbid, bOpm, bAppend, type, bLastQuery, bNoDssp, bEsmfold) { let ic = this.icn3d, me = ic.icn3dui;
         if(!bAppend && (type === undefined || type === 'target')) {
             // if a command contains "load...", the commands should not be cleared with init()
-            let bKeepCmd = (ic.bCommandLoad) ? true : false;
-            if(!ic.bStatefile) ic.init(bKeepCmd);
+            let bClearCmd = (ic.bCommandLoad) ? false : true;
+            if(!ic.bStatefile) ic.init(bClearCmd);
         }
 
         let hAtoms = await ic.loadPDBCls.loadPDB(data, pdbid, bOpm, undefined, undefined, bAppend, type, bEsmfold); // defined in the core library
@@ -127231,7 +127417,7 @@ class DcdParser {
             }
 
             for(let j in residuesOri) {
-                let idArray = j.split('_');
+                let idArray = me.utilsCls.getIdArray(j);
                 let structure2 = idArray[0] + molNum;
                 let residid2 = structure2 + '_' + idArray[1] + '_' + idArray[2];
                 ic.residues[residid2] = {};
@@ -127242,7 +127428,7 @@ class DcdParser {
             }
 
             for(let j in chainsOri) {
-                let idArray = j.split('_');
+                let idArray = me.utilsCls.getIdArray(j);
                 let structure2 = idArray[0] + molNum;
                 let chainid2 = structure2 + '_' + idArray[1];
                 
@@ -127273,7 +127459,7 @@ class DcdParser {
 
             // set ic.ncbi2resid and ic.resid2ncbi
             for(let chainid in chainsOri) {
-                let idArray = chainid.split('_');
+                let idArray = me.utilsCls.getIdArray(chainid);
                 let structure2 = idArray[0] + molNum;
                 let chainid2 = structure2 + '_' + idArray[1];
 
@@ -127837,7 +128023,7 @@ class XtcParser {
             }
 
             for(let j in residuesOri) {
-                let idArray = j.split('_');
+                let idArray = me.utilsCls.getIdArray(j);
                 let structure2 = idArray[0] + molNum;
                 let residid2 = structure2 + '_' + idArray[1] + '_' + idArray[2];
                 ic.residues[residid2] = {};
@@ -127848,7 +128034,7 @@ class XtcParser {
             }
 
             for(let j in chainsOri) {
-                let idArray = j.split('_');
+                let idArray = me.utilsCls.getIdArray(j);
                 let structure2 = idArray[0] + molNum;
                 let chainid2 = structure2 + '_' + idArray[1];
                 
@@ -127879,7 +128065,7 @@ class XtcParser {
 
             // set ic.ncbi2resid and ic.resid2ncbi
             for(let chainid in chainsOri) {
-                let idArray = chainid.split('_');
+                let idArray = me.utilsCls.getIdArray(chainid);
                 let structure2 = idArray[0] + molNum;
                 let chainid2 = structure2 + '_' + idArray[1];
 
@@ -128105,9 +128291,8 @@ class MsaParser {
 
             // realign based on residue by residue
             let alignment_final = ic.inputChainidArray.join(',');
-
             if(predefinedres && (alignment_final.split(',').length - 1) != predefinedres.split(': ').length) {
-                var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+                var aaa = 1; //alert("Please make sure the number of chains " + (alignment_final.split(',').length - 1) + " and the lines of predefined residues " + predefinedres.split(': ').length + " are the same...");
                 return;
             }
 
@@ -128165,7 +128350,7 @@ class MsaParser {
             }
 
             if(type == 'clustalw') {
-                if(line.substr(0, 1) != ' ' && line.substr(0, 1) != '\t') {
+                if(line.substr(0, 1) != '.' && line.substr(0, 1) != '*') {
                     let chainid_seq = line.split(/\s+/);
                     let idArray = chainid_seq[0].split('|');
                     let result = this.getChainid(idArray, bStart && !bSecBlock);
@@ -128190,9 +128375,11 @@ class MsaParser {
                     seq = '';
 
                     let pos = line.indexOf(' ');
+                    if(pos == -1) pos = line.length;
                     let idArray = line.substr(1, pos).split('|');
-                    
+                   
                     if(idArray.length == 1) {
+                        bFound = true;
                         chainid = idArray[0];
                     }
                     else {
@@ -128256,8 +128443,9 @@ class MsaParser {
                 ic.inputChainidArray.push(chainid + '_A');
             }
         }
-        else if(chainid.indexOf('_') != -1) { // PDB ID
-            let stru = chainid.substr(0, chainid.indexOf('_')).substr(0, 4);
+        else if(chainid.indexOf('_') != -1 || chainid.indexOf('pdb_') != -1) { // PDB ID
+            let idArray = me.utilsCls.getIdArray(chainid);
+            let stru = idArray[0];
             ic.struArray.push(stru);
             ic.inputChainidArray.push(chainid);
         }
@@ -128339,7 +128527,7 @@ class RealignParser {
                 }
 
                 // ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)).substr(0, 1)});
-                 ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn).substr(0, 1)});
+                 ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn, true)});
 
                 struct2chain[atom.structure] = atom.structure + '_' + atom.chain;
 
@@ -128382,7 +128570,8 @@ class RealignParser {
 
     async parseChainRealignPredefined(chainidArray, struct2SeqHash, struct2CoorHash, struct2resid) { let ic = this.icn3d, me = ic.icn3dui;
 
-      let toStruct = chainidArray[0].substr(0, chainidArray[0].indexOf('_')); //.toUpperCase();
+      let itemArray1 = me.utilsCls.getIdArray(chainidArray[0]);
+      let toStruct = itemArray1[0];
 
       let hAtoms = {}, rmsd;
 
@@ -128395,13 +128584,14 @@ class RealignParser {
       ic.qt_start_end = [];
 
       let chainidHash = {};
-      for(let index = 0, indexl = chainidArray.length - 1; index < indexl; ++index) {         
-          let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
+      for(let index = 0, indexl = chainidArray.length - 1; index < indexl; ++index) {    
+          let itemArray2 = me.utilsCls.getIdArray(chainidArray[index + 1]);     
+          let fromStruct = itemArray2[0];
 
           //if(toStruct == fromStruct) fromStruct += me.htmlCls.postfix;
 
-          let chainTo = toStruct + chainidArray[0].substr(chainidArray[0].indexOf('_'));
-          let chainFrom = fromStruct + chainidArray[index + 1].substr(chainidArray[index + 1].indexOf('_'));
+          let chainTo = toStruct + '_' + itemArray1[1];
+          let chainFrom = fromStruct + '_' + itemArray2[1];
           chainidHash[chainTo] = 1;
           chainidHash[chainFrom] = 1;
 
@@ -128436,7 +128626,7 @@ class RealignParser {
 
           hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
           rmsd = parseFloat(result.rmsd);
-      }
+      } 
 
       // If rmsd from vastsrv is too large, realign the chains
       //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {  
@@ -128658,15 +128848,6 @@ class RealignParser {
             prevChainid = chainidArrayTmp[i];
         }
         
-        // use the model from Membranome as template
-        // if(ic.bAfMem && chainidArray.length == 2) {
-        //     if(chainidArray[1].split('_')[0] == pdbidTemplate) {
-        //         let tmp = chainidArray[0];
-        //         chainidArray[0] = chainidArray[1]; 
-        //         chainidArray[1] = tmp;
-        //     }
-        // }
-        
         let bRealign = true;
         ic.qt_start_end = []; // reset the alignment
 
@@ -128911,12 +129092,13 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
         let predefinedResArray, predefinedResPair;
 
         if(bPredefined) {
-            me.cfg.resdef.replace(/; /gi, ': ');
-            predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split(': ');
-            // predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split('; ');
-            
+            me.cfg.resdef = decodeURIComponent(me.cfg.resdef).trim();
+            let tmpStr = me.cfg.resdef.replace(/; /gi, ': ');
+            // predefinedResArray = decodeURIComponent(tmpStr).trim().replace(/\+/gi, ' ').split(': ');
+            predefinedResArray = tmpStr.replace(/\+/gi, ' ').split(': ');
+
             if(predefinedResArray.length != chainidArray.length - 1) {
-               var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+               var aaa = 1; //alert("Please make sure the number of chains " + (chainidArray.length - 1) + " and the lines of predefined residues " + predefinedResArray.length + " are the same...");
                return;
             }
         }
@@ -128925,8 +129107,8 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
         for(let i = 0, il = chainidArray.length; i < il; ++i) {
             //if(bPredefined) predefinedRes = predefinedResArray[i].trim();
 
-            let pos = chainidArray[i].indexOf('_');
-            let mmdbid = chainidArray[i].substr(0, pos); //.toUpperCase();
+            let itemArray = me.utilsCls.getIdArray(chainidArray[i]);
+            let mmdbid = itemArray[0]; //.toUpperCase();
 
             // if(!bRealign) mmdbid =  mmdbid.toUpperCase();
 
@@ -128934,7 +129116,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                 mmdbid_t = mmdbid;
             }
 
-            let chainid = mmdbid + chainidArray[i].substr(pos);
+            let chainid = mmdbid + '_' + itemArray[1]; 
             if(i == 0) chainid_t = chainid;
             
             if(!ic.chainsSeq || !ic.chainsSeq[chainid]) {
@@ -128963,7 +129145,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                     if(!struct2CoorHash[chainidpair]) struct2CoorHash[chainidpair] = {};
                     if(!struct2resid[chainidpair]) struct2resid[chainidpair] = {};
 
-                    // master
+                    // template
                     resiArray = predefinedResPair[0].split(",");        
 
                     result = thisClass.getSeqCoorResid(resiArray, chainid_t);
@@ -128978,7 +129160,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                     struct2CoorHash[chainidpair][mmdbid_t] = struct2CoorHash[chainidpair][mmdbid_t].concat(result.coor);
                     struct2resid[chainidpair][mmdbid_t] = struct2resid[chainidpair][mmdbid_t].concat(result.resid);
 
-                    // slave
+                    // query
                     resiArray = predefinedResPair[1].split(",");
 
                     result = thisClass.getSeqCoorResid(resiArray, chainid); 
@@ -129006,7 +129188,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                 }
             }
             else {           
-                if(i == 0) { // master
+                if(i == 0) { // template
                     //base = parseInt(ic.chainsSeq[chainid][0].resi);
 
                     resiArray = [];
@@ -129046,7 +129228,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                                 bSelectedBoth = true;
 
                                 let resn = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]).resn;
-                                struct2SeqHash[chainid] += me.utilsCls.residueName2Abbr(resn);
+                                struct2SeqHash[chainid] += me.utilsCls.residueName2Abbr(resn, true);
 
                                 struct2CoorHash[chainid] = struct2CoorHash[chainid].concat(this.getResCoorArray(resid));
 
@@ -131361,9 +131543,6 @@ class LoadAtomData {
                 atm.coord = new Vector3$1(atm.coord.x, atm.coord.y, atm.coord.z);
             }
 
-            // let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn.substr(0, 3));
-            let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn);
-
             if((type === 'mmdbid' || type === 'align') && ic.bFullUi ) {
                 // set ic.mmdbMolidResid2mmdbChainResi
                 if(ic.mmdbMolidResid2mmdbChainResi === undefined) ic.mmdbMolidResid2mmdbChainResi = {};
@@ -131505,6 +131684,8 @@ class LoadAtomData {
                 }
             }
 
+            // let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn.substr(0, 3));
+            let oneLetterRes = (atm.het) ? me.utilsCls.residueName2Abbr(atm.resn) : me.utilsCls.residueName2Abbr(atm.resn, true);
             ic.residueId2Name[residueid] = oneLetterRes;
 
             let secondaries = '-';
@@ -131852,59 +132033,6 @@ class SetSeqAlign {
           ic.nconsHash2 = {};
           ic.nalignHash2 = {};
 
-          let msaSameColor = [];
-          // assume all aligned seq are the same. If any aligned res is different,set it to false (0)
-          for(let i = 0, il = seqalign[0].length; i < il; ++i) {
-            msaSameColor.push(1);
-          }
-
-          for(let i = 0, il = seqalign.length; i < il; ++i) {
-            // first sequence
-            let alignData = seqalign[i][0];
-            let molid1 = alignData.moleculeId;
-
-            let chain1 = ic.pdbid_molid2chain[mmdbid1 + '_' + molid1];
-            chainid1 = mmdbid1 + '_' + chain1;
-
-            let id2aligninfo = {};
-            let start = alignData.sequence.length, end = -1;
-            let bStart = false;
-            for(let j = 0, jl = alignData.sequence.length; j < jl; ++j) {
-                // 0: internal resi id, 1: pdb resi id, 2: resn, 3: aligned or not
-                let resi =(ic.bUsePdbNum) ? ic.ParserUtilsCls.getResi(chainid1, alignData.sequence[j][0] - 1) : alignData.sequence[j][0];
-                let resn =(alignData.sequence[j][2] === '~') ? '-' : alignData.sequence[j][2];
-                resn =(resn === ' ' || resn === '') ? 'X' : resn;
-
-                let aligned =(alignData.sequence[j][3]) ? 1 : 0;
-
-                if(aligned == 1) {
-                    if(j < start && !bStart) {
-                        start = j;
-                        bStart = true; // set start just once
-                    }
-                    if(j > end) end = j;
-                }
-
-                id2aligninfo[j] = {"resi": resi, "resn": resn, "aligned": aligned};
-            }
-
-            // second sequence
-            alignData = seqalign[i][1];
-
-            for(let j = start; j <= end; ++j) {
-                // 0: internal resi id, 1: pdb resi id, 2: resn, 3: aligned or not
-                let alignedTmp =(alignData.sequence[j][3]) ? 1 : 0; 
-
-                let aligned = id2aligninfo[j].aligned + alignedTmp; // 0 or 2
-
-                if(aligned === 2) { // aligned
-                    if(id2aligninfo[j].resn != resn) {
-                        msaSameColor[j] = 0;
-                    }
-                }
-            }
-          }
-
           for(let i = 0, il = seqalign.length; i < il; ++i) {
               // first sequence
               let alignData = seqalign[i][0];
@@ -132001,8 +132129,6 @@ class SetSeqAlign {
                           ic.nconsHash2[chainid2 + '_' + resi] = 1;
                       }
 
-                      color = (msaSameColor[j] == 0) ? '#0000FF' : '#FF0000';
-
                       // mapping, use the firstsequence as the reference structure
                       ic.chainsMapping[chainid1][chainid1 + '_' + id2aligninfo[j].resi] = id2aligninfo[j].resn + id2aligninfo[j].resi;
                       ic.chainsMapping[chainid2][chainid2 + '_' + resi] = id2aligninfo[j].resn + id2aligninfo[j].resi;
@@ -132019,8 +132145,6 @@ class SetSeqAlign {
 
                       ic.nalignHash1[chainid1 + '_' + id2aligninfo[j].resi] = 1;
                       ic.nalignHash2[chainid2 + '_' + resi] = 1;
-
-                      msaSameColor[j] = 2; // not aligned
                   }
 
                   // chain1
@@ -132400,7 +132524,7 @@ class SetSeqAlign {
                       }
                   }
               }
-
+            
               for(let j = 0; j <= end1 - start1; ++j) {
                   ///if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid2] === undefined) break;
 
@@ -132513,29 +132637,43 @@ class SetSeqAlign {
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let start1, end1;
                 
-                //ic.qt_start_end is zero-based
-                if(!bRealign && me.cfg.aligntool != 'tmalign') { // vast alignment
-                    start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
-                }
-                else {
-                    start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
-                }
-
+                // if(bRealign) { // real residue numbers are stored
+                //     start1 = ic.qt_start_end[chainIndex][i].t_start;
+                //     end1 = ic.qt_start_end[chainIndex][i].t_end;
+                // }
+                // else {
+                    //ic.qt_start_end is zero-based
+                    if(!bRealign && me.cfg.aligntool != 'tmalign') { // vast alignment
+                        start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
+                        end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
+                    }
+                    else {
+                        start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
+                        end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+                    }
+                // }
                 for(let j = start1; j <= end1; ++j) {
                     let resi, resid;
 
-                    // let resiPos;
-                    // if(me.cfg.aligntool == 'tmalign') {
-                    //     resiPos = j - baseResi;
+                    // if(me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
+                    //     resi = ic.qt_start_end[chainIndex][i].t_start;
                     // }
                     // else {
-                    //     resiPos = j;
+                        // let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
+                        // let resiPos;
+                        // if(me.cfg.aligntool == 'tmalign') {
+                        //     resiPos = j - baseResi;
+                        // }
+                        // else {
+                        //     // resiPos = (bRealign) ? j : j - baseResi;
+                        //     resiPos = j;
+                        // }
+
+                        let resiPos = j;
+
+                        resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
+                        resid = chainidArray[0] + '_' + resi;
                     // }
-                    let resiPos = j;
-                    resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
-                    resid = chainidArray[0] + '_' + resi;
 
                     resid2range_t[resid] = 1;
                     if(j < start_t) start_t = j;
@@ -132549,14 +132687,18 @@ class SetSeqAlign {
 
         let resid2rangeArray = Object.keys(resid2range_t);
         resid2rangeArray.sort(function(a, b) {
-            return parseInt(a.split('_')[2]) - parseInt(b.split('_')[2]);
+            // return parseInt(a.split('_')[2]) - parseInt(b.split('_')[2]);
+            let idArray1 = me.utilsCls.getIdArray(a);
+            let idArray2 = me.utilsCls.getIdArray(b);
+            return parseInt(idArray1[2]) - parseInt(idArray2[2]);
         });
 
         // assign range to each resi
         let prevResi = -999, start = 0, end = 0, residArray = [], prevEnd = 0;
         for(let i = 0, il = resid2rangeArray.length; i < il; ++i) {
             let resid = resid2rangeArray[i];
-            let resi = resid.split('_')[2];
+            let idArray = me.utilsCls.getIdArray(resid);
+            let resi = idArray[2];
             
             if(i == 0) {
                 start = resi;
@@ -132596,7 +132738,7 @@ class SetSeqAlign {
             let resid = chainid1 + '_' + resi;
 
             // let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
-            let jAdjusted = ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
+            let jAdjusted = (me.cfg.aligntool == 'seqalign') ? j : ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
 
             //if(j + baseResi < start_t || j + baseResi > end_t) {
             if(jAdjusted < start_t || jAdjusted > end_t) {    
@@ -132614,6 +132756,7 @@ class SetSeqAlign {
             resObject.color2 = (resid2range_t[resid]) ? '#FF0000' : me.htmlCls.GREYC; // color by conservation
             // resObject.class = (resid2range_t[resid]) ? 'icn3d-align' : 'icn3d-nalign';
             resObject.class = (resid2range_t[resid]) ? 'icn3d-cons' : 'icn3d-nalign';
+    
             ic.alnChainsSeq[chainid1].push(resObject);
 
             if(resid2range_t[resid]) {
@@ -132747,7 +132890,7 @@ class SetSeqAlign {
         if(ic.alnChainsSeq[chainid1]) {
             for(let j = 0, jl = ic.alnChainsSeq[chainid1].length; j < jl; ++j) {
                 //add gap before the mapping region       
-                //if(parseInt(ic.alnChainsSeq[chainid1][j].resi) == parseInt(resi_t)) {
+                // if(parseInt(ic.alnChainsSeq[chainid1][j].resi) == parseInt(resi_t)) {
                 if(ic.alnChainsSeq[chainid1][j].resi == resi_t) {
                     pos_t = j;
                     break;
@@ -132773,7 +132916,6 @@ class SetSeqAlign {
         for(let j = 0, jl = alignedChainIndice.length - 1; j < jl; ++j) {
             let chainidTmp = chainidArray[alignedChainIndice[j]];
             let gapResObject = this.getResObject(chainidTmp, true);
-            
             //for(let k = 0, kl = len - nGap; k < kl; ++k) {
             for(let k = 0, kl = len; k < kl; ++k) {
                 ic.alnChainsSeq[chainidTmp].splice(pos_t, 0, gapResObject);
@@ -132790,6 +132932,7 @@ class SetSeqAlign {
             // let resn2 = this.getResn(chainid, start + j);
             let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start + j : ic.ParserUtilsCls.getResi(chainid, start + j);
             let resn2 = this.getResnFromResi(chainid, resi2);
+
             let resn1 = '-';
             let bAlign = false;
             let resObject = this.getResObject(chainid, false, bAlign, resi2, resn2, resn1);
@@ -132797,9 +132940,17 @@ class SetSeqAlign {
         }
     }
 
+    getTemplatePosFromOriPos(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
+        let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
+        let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
+            
+        let result1 = this.getResiPosInTemplate(chainid1, startResi);
+        let result2 = this.getResiPosInTemplate(chainid1, endResi);
+        
+        return {"pos1": result1.pos, "pos2": result2.pos};
+    }
+
     getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
-        // let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
-        // let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
         if(bRealign && me.cfg.aligntool == 'tmalign') { // vast alignment
             let startResi = start;
             let endResi = end;
@@ -132873,9 +133024,6 @@ class SetSeqAlign {
         if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
 
         let result;
-
-        let nGapInTemplate = 0; // number of gaps inserted into the template sequence
-        let startPosInTemplate = 0; // position in the template sequence to start the mapping
         
         // need to improve when tmalign with residue number with postfix such as 52A in 4ORZ_C,5ESV_H
         // start and end should be positions, not original residue numbers.
@@ -132885,8 +133033,7 @@ class SetSeqAlign {
         }
 
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
-            let start1, start2, end1, end2, resiStart1, start1Pos;
-          
+            let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
             if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
@@ -132901,7 +133048,7 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = start1;
                 start1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_start);
-                this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
+                end1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
             }
             else {
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start - 1);
@@ -132912,28 +133059,49 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = ic.ParserUtilsCls.getResi(chainid1, start1);
                 start1Pos = start1;
+                end1Pos = end1;
             }
             //let range = resid2range_t[chainid1 + '_' + resiStart1];
-
+  
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
-                startPosInTemplate = start1Pos;
 
-                result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
-                //result = this.getTemplatePosFromOriResi(chainid1, start_t, start1Pos, bRealign);
-                pos1 = result.pos1;
-                pos2 = result.pos2;
+                if(me.cfg.aligntool == 'seqalign') {
+                    result = this.getTemplatePosFromOriPos(chainid1, start_t, start1Pos, bRealign);
 
-                if(start1 > start_t) {
-                //if(start1Pos > start_t) {
-                    for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
-                        ic.alnChainsSeq[chainid2].push(gapResObject2);
+                    pos1 = result.pos1;
+                    pos2 = result.pos2;
+                    
+                    //if(start1 > start_t) {
+                    if(start1Pos > start_t) {
+                        for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
+                            ic.alnChainsSeq[chainid2].push(gapResObject2);
+                        }
+                    }
+                }
+                else {
+                    result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
+
+                    pos1 = result.pos1;
+                    pos2 = result.pos2;
+                    
+                    if(start1 > start_t) {
+                    //if(start1Pos > start_t) {
+                        for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
+                            ic.alnChainsSeq[chainid2].push(gapResObject2);
+                        }
                     }
                 }
             }
             else {
                 //let notAlnLen1 = start1 - (prevIndex1 + 1);
-                result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, start1, bRealign);
+                //!!!
+                if(me.cfg.aligntool == 'seqalign') {
+                    result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, start1Pos, bRealign);
+                }
+                else {
+                    result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, start1, bRealign);
+                }
                 pos1 = result.pos1;
                 pos2 = result.pos2;
                 let notAlnLen1 = pos2 - (pos1 + 1);
@@ -132944,46 +133112,48 @@ class SetSeqAlign {
 
                 // insert non-aligned residues in query seq
                 this.insertNotAlignRes(chainid2, prevIndex2+1, notAlnLen2, bRealign);
+
                 if(notAlnLen1 >= notAlnLen2) {
                     // add gaps before the query sequence
                     for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
                         ic.alnChainsSeq[chainid2].push(gapResObject2);
-                    }
+                    }                       
                 }
                 else {
                     // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
                     this.addGapAllAlnChains(chainidArray, alignedChainIndice, chainid1, resiStart1, notAlnLen2 - notAlnLen1);
-                    nGapInTemplate += (notAlnLen2 - notAlnLen1);
                 }                           
             }
 
             // 2. In the mapped residues
-            result = this.getTemplatePosFromOriResi(chainid1, start1, end1, bRealign);
-            //result = this.getTemplatePosFromOriResi(chainid1, start1Pos, end1Pos, bRealign);
+            if(me.cfg.aligntool == 'seqalign') {
+                result = this.getTemplatePosFromOriPos(chainid1, start1Pos, end1Pos, bRealign);
+            }
+            else {
+                result = this.getTemplatePosFromOriResi(chainid1, start1, end1, bRealign);
+            }
             pos1 = result.pos1;
             pos2 = result.pos2;
-
+            
             let k = 0;    
             if(!ic.chainsMapping[chainid1]) ic.chainsMapping[chainid1] = {};
             if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
-            let resiAdjust = (bRealign && me.cfg.aligntool == 'tmalign') ? 0 : - startPosInTemplate + nGapInTemplate; 
             for(let j = pos1; j <= pos2; ++j) {
                 // inherit the gaps from the template
-                if(ic.alnChainsSeq[chainid1][j + resiAdjust].resn == '-') {
+                if(ic.alnChainsSeq[chainid1][j].resn == '-') {
                     ic.alnChainsSeq[chainid2].push(gapResObject2);
                 }
                 else {                   
                     let resi1 = (bRealign && me.cfg.aligntool == 'tmalign') ? start1 + k : ic.ParserUtilsCls.getResi(chainid1, start1 + k);
                     let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
-
                     let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
                     let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
-
+                    
                     let bAlign = true;
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
                     ic.alnChainsSeq[chainid2].push(resObject);
                     // update color in the template
-                    ic.alnChainsSeq[chainid1][j + resiAdjust].color = resObject.color;
+                    ic.alnChainsSeq[chainid1][j].color = resObject.color;
 
                     ic.chainsMapping[chainid1][chainid1 + '_' + resi1] = resn1 + resi1;
                     ic.chainsMapping[chainid2][chainid2 + '_' + resi2] = resn1 + resi1;  
@@ -133001,7 +133171,12 @@ class SetSeqAlign {
         } 
 
         // add gaps at the end
-        result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, end_t, bRealign);
+        if(me.cfg.aligntool == 'seqalign') {
+            result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
+        }
+        else {
+            result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, end_t, bRealign);
+        }
         pos1 = result.pos1;
         pos2 = result.pos2;
         for(let i = pos1; i < pos2; ++i) {
@@ -133021,7 +133196,7 @@ class SetSeqAlign {
 
         for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
-
+            
             start1 = ic.qt_start_end[index][i].t_start;
             start2 = ic.qt_start_end[index][i].q_start;
             end1 = ic.qt_start_end[index][i].t_end;
@@ -133339,8 +133514,8 @@ class SetSeqAlign {
 
     setMsaFormat(chainidArray) { let ic = this.icn3d; ic.icn3dui;
         //set MSA
-        let fastaFormat = '', clustalwFormat = 'CLUSTALWW\n\n', resbyresFormat = '';
-        let chainArrayClustal = [];
+        let fastaFormat = '', clustalwFormat = 'CLUSTALW\n\n', resbyresFormat = '';
+        let chainArrayClustalw = [];
         
         let consArray = [], resiArrayTemplate = [];
         let chainidTemplate = chainidArray[0];
@@ -133409,8 +133584,8 @@ class SetSeqAlign {
 
             fastaFormat += '\n';
 
-            chainArrayClustal.push(clustalwArray);
-            if(i == il - 1) chainArrayClustal.push(consArray);
+            chainArrayClustalw.push(clustalwArray);
+            if(i == il - 1) chainArrayClustalw.push(consArray);
 
             // residue by residue
             let resiRangeStr1 = ic.resid2specCls.resi2range(resiArrayTarget, true);
@@ -133419,10 +133594,10 @@ class SetSeqAlign {
             if(i > 0) resbyresFormat += resiRangeStr1 + ' | ' + resiRangeStr2 + '\n';
         }
 
-        // CLUSTALWW
-        for(let j = 0, jl = chainArrayClustal[0].length; j < jl; ++j) {
-            for(let i = 0, il = chainArrayClustal.length; i < il; ++i) {
-                clustalwFormat += chainArrayClustal[i][j] + '\n';
+        // CLUSTALW
+        for(let j = 0, jl = chainArrayClustalw[0].length; j < jl; ++j) {
+            for(let i = 0, il = chainArrayClustalw.length; i < il; ++i) {
+                clustalwFormat += chainArrayClustalw[i][j] + '\n';
             }
             clustalwFormat += '\n';
         }
@@ -133889,7 +134064,7 @@ class LoadPDB {
                 //if(residueNum !== prevResidueNum) {
                     
                 if(oriResidueNum !== prevOriResidueNum) {
-                    let residue = me.utilsCls.residueName2Abbr(resn);
+                    let residue = (atomDetails.het) ? me.utilsCls.residueName2Abbr(resn) : me.utilsCls.residueName2Abbr(resn, true);
                     ic.residueId2Name[residueNum] = residue;
 
                     if(serial !== 1 && prevResidueNum !== '') ic.residues[prevResidueNum] = residuesTmp;
@@ -134336,7 +134511,7 @@ class LoadPDB {
 
         for(let chainid in chains) {
             if(pdbid !== undefined) {
-                let textArray =  chainid.split('_');
+                let textArray =  me.utilsCls.getIdArray(chainid);
                 if(textArray[0] !== pdbid) continue; // skip different chain
             }
 
@@ -134444,15 +134619,15 @@ class LoadCIF {
     loadCIF(bcifData, bcifid, bText, bAppend, supercell) { let ic = this.icn3d, me = ic.icn3dui;
         ic.cifText = bText;
         ic.cifData = bcifData;
-        
+
         if(supercell === undefined) {
-            CIFTools.Text.coreCifOptions = { nx: 1, ny: 1, nz: 1, boundary: true };
+            CIFTools.Text.coreCifOptions = { nx: 1, ny: 1, nz: 1, boundary: true, wholeMolecules: true, bondTolerance: 0.4 };
         }
         else if(supercell === 0) {
-            CIFTools.Text.coreCifOptions = { nx: 1, ny: 1, nz: 1, boundary: false };
+            CIFTools.Text.coreCifOptions = { nx: 1, ny: 1, nz: 1, boundary: true, wholeMolecules: true, bondTolerance: 0.4 };
         }
         else {
-            CIFTools.Text.coreCifOptions = { nx: supercell, ny: supercell, nz: supercell, boundary: true };
+            CIFTools.Text.coreCifOptions = { nx: supercell, ny: supercell, nz: supercell, boundary: true, wholeMolecules: true, bondTolerance: 0.4 };
         }
 
         let hAtoms = {};
@@ -134468,7 +134643,7 @@ class LoadCIF {
         let serial, moleculeNum;
         // if(!bMutation && !bAppend) {
         if(!bAppend) {
-            ic.init();
+            ic.init(undefined, true); // keep original configurations, such as color, style, etc. when loading multiple structures
             moleculeNum = 0; //1;
             serial = 0;
         }
@@ -134512,11 +134687,13 @@ class LoadCIF {
 
             if (parsed.isError) {
                 // report error:
-                var aaa = 1; //alert("The Binary CIF data can NOT be parsed: " + parsed.toString());
+                var aaa = 1; //alert("2 The Binary CIF data can NOT be parsed: " + parsed.toString());
                 return;
             }
 
             let block = parsed.result.dataBlocks[0];
+
+            if(!block) continue;
             
             if(block.getCategory("_entry")) {
                 id = block.getCategory("_entry").getColumn("id").getString(0);
@@ -134755,6 +134932,8 @@ class LoadCIF {
                 ic.cell.angle_alpha = parseFloat(block.getCategory("_cell").getColumn("angle_alpha").getString(0));
                 ic.cell.angle_beta = parseFloat(block.getCategory("_cell").getColumn("angle_beta").getString(0));
                 ic.cell.angle_gamma = parseFloat(block.getCategory("_cell").getColumn("angle_gamma").getString(0));
+
+                me.htmlCls.clickMenuCls.setLogCmd("define unitcell | " + ic.cell.length_a + " | " + ic.cell.length_b + " | " + ic.cell.length_c + " | " + ic.cell.angle_alpha + " | " + ic.cell.angle_beta + " | " + ic.cell.angle_gamma, true);
             }
 
             // if (record === 'ENDMDL') {
@@ -135099,7 +135278,7 @@ class LoadCIF {
                     
                 // if(oriResidueNum !== prevOriResidueNum) {
                 if(oriResidueNum !== prevOriResidueNum || chain + "_" + resn != prevResn || prevAutochain != autochain) {
-                    let residue = me.utilsCls.residueName2Abbr(resn);
+                    let residue = (atomDetails.het) ? me.utilsCls.residueName2Abbr(resn) : me.utilsCls.residueName2Abbr(resn, true);
                    
                     ic.residueId2Name[residueNum] = residue;
 
@@ -136398,6 +136577,16 @@ class ApplyCommand {
         ic.opts['unitcell'] = 'no';
         ic.drawCls.draw();
       }
+      else if(command.indexOf('define unitcell') !== -1) {
+        let itemArray = command.split(' | ');
+        ic.cell = {};
+        ic.cell.length_a = parseFloat(itemArray[1]);
+        ic.cell.length_b = parseFloat(itemArray[2]);
+        ic.cell.length_c = parseFloat(itemArray[3]);
+        ic.cell.angle_alpha = parseFloat(itemArray[4]);
+        ic.cell.angle_beta = parseFloat(itemArray[5]);
+        ic.cell.angle_gamma = parseFloat(itemArray[6]);
+      }
       else if(command == 'set fog on') {
         ic.opts['fog'] = 'yes';
         ic.fogCls.setFog(true);
@@ -136428,7 +136617,7 @@ class ApplyCommand {
         let pos = command.lastIndexOf(' ');
         let supercell = parseInt(command.substr(pos + 1));
 
-        await me.htmlCls.clickMenuCls.setSupercell(supercell);
+        me.htmlCls.clickMenuCls.setSupercell(supercell);
       }
       else if(command == 'set chemicalbinding show') {
         ic.setOptionCls.setOption('chemicalbinding', 'show');
@@ -136863,7 +137052,8 @@ class ApplyCommand {
       else if(commandOri.indexOf('select interaction') == 0) {
         let idArray = commandOri.substr(commandOri.lastIndexOf(' ') + 1).split(',');
         if(idArray !== null) {
-            let mmdbid = idArray[0].split('_')[0];
+            let itemArray = me.utilsCls.getIdArray(idArray[0]);
+            let mmdbid = itemArray[0];
             if(!ic.b2DShown) ic.ParserUtilsCls.download2Ddgm(mmdbid.toUpperCase());
 
             ic.diagram2dCls.selectInteraction(idArray[0], idArray[1]);
@@ -138709,7 +138899,7 @@ class DefinedSets {
 
     }
 
-    selectCombinedSets(strSets, commandname) { let ic = this.icn3d; ic.icn3dui;
+    selectCombinedSets(strSets, commandname) { let ic = this.icn3d, me = ic.icn3dui;
         let idArray = strSets.split(' ');
 
         let orArray = [], andArray = [], notArray = [];
@@ -138717,7 +138907,7 @@ class DefinedSets {
 
         for(let i = 0, il = idArray.length; i < il; ++i) {
             // replace 1CD8_A_1 with 1CD8_A1
-            let tmpArray = idArray[i].split('_');
+            let tmpArray = me.utilsCls.getIdArray(idArray[i]);
             if(tmpArray.length == 3 && !isNaN(tmpArray[2])) {
                 idArray[i] = tmpArray[0] + '_' + tmpArray[1] + tmpArray[2];
             }
@@ -139719,7 +139909,7 @@ class LoadScript {
 
         // load pdb, mmcif, mmdb, cid
         let id = loadStr.substr(loadStr.lastIndexOf(' ') + 1);
-        if(id.length == 4) id = id.toUpperCase();
+        if(id.length == 4 || id.indexOf('pdb_') == 0) id = id.toUpperCase();
 
         // skip loading the structure if 
         // 1. PDB was in the iCn3D PNG Image file
@@ -139766,6 +139956,10 @@ class LoadScript {
           me.cfg.mmcifid = id;
           await ic.mmcifParserCls.downloadMmcif(id);
         }
+        else if(command.indexOf('load cod') !== -1) {
+          me.cfg.codid = id;
+          await ic.mmcifParserCls.downloadCod(id);
+        }
         else if(command.indexOf('load mmdb ') !== -1 || command.indexOf('load mmdb1 ') !== -1) {
           me.cfg.mmdbid = id;
           me.cfg.bu = 1;
@@ -140280,7 +140474,7 @@ class SelectByCommand {
 
            // convert 1TOP_A:20 to $1TOP.A:20
            if(commandArray[i].indexOf('_') !== -1) {
-             let itemArray = commandArray[i].split('_');
+             let itemArray = me.utilsCls.getIdArray(commandArray[i]);
              if(itemArray.length ==2 ) {
               commandArray[i] = '$' + itemArray[0] + '.' + itemArray[1];
              }
@@ -141527,6 +141721,15 @@ class Resid2spec {
          return Object.keys(residueHash);
     }
 
+    atoms2chains(atoms) {var ic = this.icn3d; ic.icn3dui;
+         let chains = {};
+         for(let i in atoms) {
+             let atom = ic.atoms[i];
+             chains[atom.structure + '_' + atom.chain] = 1;
+         }
+         return chains;
+    }
+
     atoms2structureArray(atoms) {var ic = this.icn3d; ic.icn3dui;
          let structures = {};
          for(let i in atoms) {
@@ -143161,24 +143364,6 @@ class Dssp {
                 if(!me.bNode) console.log("domainid: " + domainid);
             }
 
-            // count the number of matched strands
-            // let strandHash = {};
-            // for(let j = 0, jl = queryData[0].segs.length; j < jl; ++j) {
-            //     let seg = queryData[0].segs[j];
-            //     let q_start = parseInt(seg.q_start)
-
-            //     let strand = this.getStrandFromRefnum(q_start);
-            //     strandHash[strand] = 1;
-            // }
-
-            // let tmAdjust = 0.1; 
-
-            // if the TM score difference is within 0.1 and more strands are found, use the template with more strands
-            // if(!domainid2segs.hasOwnProperty(domainid) || 
-            //     (score >= parseFloat(ic.domainid2score[domainid].split('_')[0]) + tmAdjust)
-            //     || (score >= parseFloat(ic.domainid2score[domainid].split('_')[0]) - tmAdjust && score < parseFloat(ic.domainid2score[domainid].split('_')[0]) + tmAdjust && Object.keys(strandHash).length > domainid2strandcnt[domainid])
-            //     ) {
-
             // use TM-score alone
             if(!domainid2segs.hasOwnProperty(domainid) || score >= parseFloat(ic.domainid2score[domainid].split('_')[0])) {      
                 ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res + '_' + queryData[0].score2;
@@ -144510,7 +144695,7 @@ class Scap {
         let snpArray = snp.split(','); //stru_chain_resi_snp
         let atomHash = {}, snpResidArray = [], chainResi2pdb = {};
         for(let i = 0, il = snpArray.length; i < il; ++i) {
-            let idArray = snpArray[i].split('_'); //stru_chain_resi_snp
+            let idArray = me.utilsCls.getIdArray(snpArray[i]); //stru_chain_resi_snp
 
             let resid = idArray[0] + '_' + idArray[1] + '_' + idArray[2];
             atomHash = me.hashUtilsCls.unionHash(atomHash, ic.residues[resid]);
@@ -147662,7 +147847,8 @@ class Diagram2d {
             if(refnumLabel) {
                 refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                 if(!ic.refnum2resn[domainid]) ic.refnum2resn[domainid] = {};
-                ic.refnum2resn[domainid][refnumStr] = resn + resid.split('_')[2];
+                let idArray = me.utilsCls.getIdArray(resid);
+                ic.refnum2resn[domainid][refnumStr] = resn + idArray[2];
             }
         }
 
@@ -149159,10 +149345,10 @@ class ResizeCanvas {
                 //me.htmlCls.HEIGHT = $( window ).height();
                 me.utilsCls.setViewerWidthHeight(ic.icn3dui);
 
-                let width = me.htmlCls.WIDTH; // - me.htmlCls.LESSWIDTH_RESIZE;
-                let height = me.htmlCls.HEIGHT; // - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT;
+                me.htmlCls.WIDTH; // - me.htmlCls.LESSWIDTH_RESIZE;
+                me.htmlCls.HEIGHT; // - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT;
 
-                if(ic !== undefined && !ic.bFullscreen) thisClass.resizeCanvas(width, height);
+                //if(ic !== undefined && !ic.bFullscreen) thisClass.resizeCanvas(width, height, true, true);
             });
         }
     }
@@ -153912,8 +154098,8 @@ class iCn3D {
   }
 }
 //When users first load a structure, call this function to empty previous settings.
-iCn3D.prototype.init = function (bKeepCmd) {
-    this.init_base();
+iCn3D.prototype.init = function (bClearCmd, bKeepConfig) {
+    this.init_base(bClearCmd, bKeepConfig);
 
     this.molTitle = "";
 
@@ -153933,8 +154119,8 @@ iCn3D.prototype.init = function (bKeepCmd) {
     this.axes = [];
 };
 
-iCn3D.prototype.init_base = function (bKeepCmd) {
-    this.resetConfig();
+iCn3D.prototype.init_base = function (bClearCmd, bKeepConfig) {
+    if(!bKeepConfig) this.resetConfig();
     
     this.structures = {}; // structure name -> array of chains
     this.chains = {}; // structure_chain name -> atom hash
@@ -154028,7 +154214,7 @@ iCn3D.prototype.init_base = function (bKeepCmd) {
     this.transformCls.rotateCount = 0;
     this.transformCls.rotateCountMax = 20;
 
-    if(bKeepCmd) this.commands = [];
+    if(bClearCmd) this.commands = [];
 
     this.axes = [];
 
@@ -154124,7 +154310,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.54.3';
+    this.REVISION = '3.54.4';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -154220,9 +154406,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
       resize: function( event, ui ) {
         me.htmlCls.WIDTH = ui.size.width; //$("#" + ic.pre + "canvas").width();
         me.htmlCls.HEIGHT = ui.size.height; //$("#" + ic.pre + "canvas").height();
-        if(ic !== undefined && !me.icn3d.bFullscreen) {
-            ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
-        }
+        // if(ic !== undefined && !me.icn3d.bFullscreen) {
+        //     ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
+        // }
       }
     });
 
@@ -154326,7 +154512,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
             let domainidArray = me.cfg.matchedchains.split(',');
             let chainidArray = [];
             for(let i = 0, il = domainidArray.length; i  < il; ++i) {
-                let idArray = domainidArray[i].split('_');
+                let idArray = me.utilsCls.getIdArray(domainidArray[i]);
                 chainidArray.push(idArray[0] + '_' + idArray[1]);
             }
 
@@ -154369,14 +154555,14 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         await ic.pdbParserCls.downloadUrl(url, type, me.cfg.command);
     }
     else if(me.cfg.mmtfid !== undefined) {
-        if(me.cfg.mmtfid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.mmtfid = me.cfg.mmtfid.substr(8); // temperary support long PDB ID such as pdb_00001tup
+        // if(me.cfg.mmtfid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.mmtfid = me.cfg.mmtfid.substr(8); // temperary support long PDB ID such as pdb_00001tup
        ic.inputid = me.cfg.mmtfid;
        ic.loadCmd = 'load mmtf ' + me.cfg.mmtfid;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
        await ic.bcifParserCls.downloadBcif(me.cfg.mmtfid);
     }
     else if(me.cfg.bcifid !== undefined) {
-        if(me.cfg.bcifid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.bcifid = me.cfg.bcifid.substr(8); // temperary support long PDB ID such as pdb_00001tup
+        // if(me.cfg.bcifid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.bcifid = me.cfg.bcifid.substr(8); // temperary support long PDB ID such as pdb_00001tup
         ic.inputid = me.cfg.bcifid;
         ic.loadCmd = 'load bcif ' + me.cfg.bcifid;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
@@ -154551,6 +154737,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         await ic.mmcifParserCls.downloadMmcif(me.cfg.mmcifid);
     }
+    else if(me.cfg.codid !== undefined) {
+        ic.inputid = me.cfg.codid;
+        ic.loadCmd = 'load cod ' + me.cfg.codid;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        await ic.mmcifParserCls.downloadCod(me.cfg.codid);
+    }
     else if(me.cfg.align !== undefined) {
         // ic.bNCBI = true;
         if(me.cfg.align.indexOf('185055,') != -1) {
@@ -154711,6 +154903,8 @@ iCn3DUI.prototype.getXMLHttpRqstPromise = function(url, dataType, responseType,
 
                    reject('error');
                 }
+
+                me.icn3d.ParserUtilsCls.hideLoading();
             }
             else {
                 me.icn3d.ParserUtilsCls.showLoading();
@@ -154863,18 +155057,6 @@ iCn3DUI.prototype.setDialogAjax = function() { let me = this;
     });
 };
 
-/*
-iCn3DUI.prototype.setIcn3dui = function(id) { let me = this;
-    let idArray = id.split('_'); // id: div0_reload_pdbfile
-    ic.pre = idArray[0] + "_";
-    if(window.icn3duiHash !== undefined && window.icn3duiHash.hasOwnProperty(idArray[0])) { // for multiple 3D display
-       me = window.icn3duiHash[idArray[0]];
-    }
-    return me;
-};
-*/
-
-
 // required by npm
 class printMsg {
   constructor() {