icn3d 3.30.3 → 3.30.5

package/icn3d.js

@@ -5828,7 +5828,7 @@ class ClickMenu {
       if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
       await ic.annotationCls.setAnnoTabIg(bSelection, template);
 
-      // ic.bRunRefnumAgain = false;
+      ic.bRunRefnumAgain = false;
     }
 
     clickMenu1() { let me = this.icn3dui; me.icn3d;
@@ -7414,7 +7414,7 @@ class ClickMenu {
             //    ic.drawCls.draw();
             // }
 
-            // ic.bRunRefnumAgain = false;
+            ic.bRunRefnumAgain = false;
          });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
@@ -11983,17 +11983,17 @@ class SetDialog {
 
     setTemplateMenu()  { let me = this.icn3dui; me.icn3d;
         let group2tpl = {};
-        group2tpl['V'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PDL1_4z18B_human_V-n1', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
-        group2tpl['C1'] = ['B2Microglobulin_7phrL_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
-        group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
-        group2tpl['I'] = ['BTLA_2aw2A_human_Iset', 'CD19_6al5A_human_C2orV-n1', 'JAM1_1nbqA_human_VorIset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152'];
-        group2tpl['E'] = ['ASF1A_2iijA_human', 'CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'TEAD1_3kysC_human'];
+        group2tpl['IgV'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
+        group2tpl['IgC1'] = ['B2Microglobulin_7phrL_human_C1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'LAG3_7tzgD_human_C1-n2', 'MHCIa_7phrH_human_C1', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_C1-n2'];
+        group2tpl['IgC2'] = ['CD2_1hnfA_human_C2-n2', 'CD3g_6jxrg_human_C2'];
+        group2tpl['IgI'] = ['BTLA_2aw2A_human_Iset', 'Contactin1_3s97C_human_Iset-n2', 'JAM1_1nbqA_human_Iset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152'];
+        group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
 
-        group2tpl['FN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
+        group2tpl['IgFN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
 
-        group2tpl['FN3-like'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
+        group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TEAD1_3kysC_human'];
 
-        group2tpl['Other'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];  
+        group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];  
 
         let tpl2strandsig = {};
         tpl2strandsig['ASF1A_2iijA_human']                          = "A A' B C C' E F G G+";
@@ -12001,17 +12001,17 @@ class SetDialog {
         tpl2strandsig['BArrestin1_4jqiA_rat_n1']                    = "A- A A' B C C' E F G";
         tpl2strandsig['BTLA_2aw2A_human_Iset']                      = "A A' B C C' D E F G";
         tpl2strandsig['C3_2qkiD_human_n1']                          = "A A' B C C' E F G";
-        tpl2strandsig['CD19_6al5A_human_C2orV-n1']                  = "A' B C C' D E F G";
+        tpl2strandsig['CD19_6al5A_human-n1']                  = "A' B C C' D E F G";
         tpl2strandsig['CD28_1yjdC_human_V']                         = "A A' B C C' C'' D E F G";
         tpl2strandsig['CD2_1hnfA_human_C2-n2']                      = "A B C C' E F G";
         tpl2strandsig['CD2_1hnfA_human_V-n1']                       = "A' B C C' C'' D E F G";
-        tpl2strandsig['CD3d_6jxrd_human_Iset']                      = "A B C D E F G";
-        tpl2strandsig['CD3e_6jxrf_human_Iset']                      = "A B C C' D E F G";
-        tpl2strandsig['CD3g_6jxrg_human_Iset']                      = "A B C C' E F G G+";
+        tpl2strandsig['CD3d_6jxrd_human_C1']                      = "A B C D E F G";
+        tpl2strandsig['CD3e_6jxrf_human_C1']                      = "A B C C' D E F G";
+        tpl2strandsig['CD3g_6jxrg_human_C2']                      = "A B C C' E F G G+";
         tpl2strandsig['CD8a_1cd8A_human_V']                         = "A A' B C C' C'' D E F G";
         tpl2strandsig['CoAtomerGamma1_1r4xA_human']                 = "A- A B C D E F G";
         tpl2strandsig['Contactin1_2ee2A_human_FN3-n9']              = "A A' B C C' E F G";
-        tpl2strandsig['Contactin1_3s97C_human_C2-n2']               = "A A' B C D E F G";
+        tpl2strandsig['Contactin1_3s97C_human_Iset-n2']               = "A A' B C D E F G";
         tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human']        = "A- A B C C' E F G";
         tpl2strandsig['ECadherin_4zt1A_human_n2']                   = "A' B C D E F G";
         tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
@@ -12019,15 +12019,15 @@ class SetDialog {
         tpl2strandsig['FAB-HEAVY_5esv_V-n1']                        = "A B C C' C'' D E F G";
         tpl2strandsig['FAB-LIGHT_5esv_C1-n2']                       = "A B C C' E F G";
         tpl2strandsig['FAB-LIGHT_5esv_V-n1']                        = "A A' B C C' C'' D E F G";
-        tpl2strandsig['GHR_1axiB_human_FN3-n1']                     = "A B C C' D E F G";
+        tpl2strandsig['GHR_1axiB_human_C1-n1']                     = "A B C C' D E F G";
         tpl2strandsig['ICOS_6x4gA_human_V']                         = "A B C C' C'' D E F G";
         tpl2strandsig['IL6Rb_1bquB_human_FN3-n2']                   = "A B C C' E F G";
         tpl2strandsig['IL6Rb_1bquB_human_FN3-n3']                   = "A B C C' E F G";
         tpl2strandsig['InsulinR_8guyE_human_FN3-n1']                = "A B C C' E F G";
         tpl2strandsig['InsulinR_8guyE_human_FN3-n2']                = "A B C C' E F G";
         tpl2strandsig['IsdA_2iteA_bacteria']                        = "A- A B C C' D E F G";
-        tpl2strandsig['JAM1_1nbqA_human_VorIset-n2']                = "A A' B C C' D E F G";
-        tpl2strandsig['LAG3_7tzgD_human_C2-n2']                     = "A A' B C C' D E F G";
+        tpl2strandsig['JAM1_1nbqA_human_Iset-n2']                = "A A' B C C' D E F G";
+        tpl2strandsig['LAG3_7tzgD_human_C1-n2']                     = "A A' B C C' D E F G";
         tpl2strandsig['LAG3_7tzgD_human_V-n1']                      = "A' B C C' D E F G";
         tpl2strandsig['LaminAC_1ifrA_human']                        = "A- A B C C' E E+ F G";
         tpl2strandsig['MHCIa_7phrH_human_C1']                       = "A B C C' D E F G";
@@ -12041,16 +12041,16 @@ class SetDialog {
         tpl2strandsig['RBPJ_6py8C_human_Unk-n1']                    = "A A' B C C' E F G";
         tpl2strandsig['RBPJ_6py8C_human_Unk-n2']                    = "A B C D E F G";
         tpl2strandsig['Sidekick2_1wf5A_human_FN3-n7']               = "A B C C' E F G";
-        tpl2strandsig['Siglec3_5j0bB_human_C2-n2']                  = "A A' B C D E F G";
+        tpl2strandsig['Siglec3_5j0bB_human_C1-n2']                  = "A A' B C D E F G";
         tpl2strandsig['TCRa_6jxrm_human_C1-n2']                     = "A B C D E F G";
         tpl2strandsig['TCRa_6jxrm_human_V-n1']                      = "A A' B C C' C'' D E F G";
         tpl2strandsig['TEAD1_3kysC_human']                          = "A A+ A' B C C' E F G G+";
         tpl2strandsig['TP34_2o6cA_bacteria']                        = "A- A B C C' D E F G";
         tpl2strandsig['TP47_1o75A_bacteria']                        = "A B C C' D E F G";
-        tpl2strandsig['Titin_4uowM_human_Unk-n152']                 = "A A' B C C' D E F G";
+        tpl2strandsig['Titin_4uowM_human_Iset-n152']                 = "A A' B C C' D E F G";
         tpl2strandsig['VISTA_6oilA_human_V']                        = "A A' B C C' C'' D E F G G+";
         tpl2strandsig['VNAR_1t6vN_shark_V']                         = "A A' B C C' D E F G";
-        tpl2strandsig['VTCN1_Q7Z7D3_human_V-n2']                    = "A B C C' D E F G G+";
+        tpl2strandsig['VTCN1_Q7Z7D3_human_C1-n2']                    = "A B C C' D E F G G+";
 
         let html = '';
         for(let group in group2tpl) {
@@ -14993,7 +14993,7 @@ class AlignSeq {
         alignChainArray = Object.keys(ic.alnChains);
 
         if (bReverse) alignChainArray = alignChainArray.reverse();
-
+        
         let maxSeqCnt = 0;
 
         let chainHash = {};
@@ -37720,8 +37720,6 @@ class AnnoIg {
         $("#" + ic.pre + "dt_" + type + "_" + chnid).html(html);
         $("#" + ic.pre + "ov_" + type + "_" + chnid).html(html2);
         $("#" + ic.pre + "tt_" + type + "_" + chnid).html(html3);
-
-        ic.bRunRefnumAgain = false;
     }
 
     showAllRefNum(giSeq, chnid) {  let ic = this.icn3d; ic.icn3dui;
@@ -42509,7 +42507,7 @@ class Annotation {
 
         ic.bRunRefnumAgain = true;
         await this.updateIg();
-        // ic.bRunRefnumAgain = false;
+        ic.bRunRefnumAgain = false;
 
         this.updateInteraction();
     }
@@ -42591,8 +42589,9 @@ class Annotation {
 
             $("[id^=" + ic.pre + "transmem]").show();
         }
-        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked) {
-            // ic.bRunRefnumAgain = true;
+        if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked || ic.bShowRefnum) {
+            // no need to redo ref num calculation
+            ic.bRunRefnumAgain = false;
 
             await this.updateIg();
 
@@ -42705,6 +42704,7 @@ class Annotation {
         if($("#" + ic.pre + "anno_transmem").length) $("#" + ic.pre + "anno_transmem")[0].checked = false;
     }
     async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d; ic.icn3dui;
+
         await this.updateIg(bSelection, template);
 
         $("[id^=" + ic.pre + "ig]").show();
@@ -42867,7 +42867,7 @@ class Annotation {
                 await thisClass.setAnnoTabIg();
                 me.htmlCls.clickMenuCls.setLogCmd("set annotation ig", true);
 
-                // ic.bRunRefnumAgain = false;
+                ic.bRunRefnumAgain = false;
             }
             else {
                 thisClass.hideAnnoTabIg();
@@ -49091,7 +49091,7 @@ class ChainalignParser {
         await this.downloadChainalignmentPart3(chainresiCalphaHash2, chainidArray, ic.hAtoms);
     }
 
-    setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
+    setMsa(chainidArray, bVastplus, bRealign) { let ic = this.icn3d, me = ic.icn3dui;        
         // get aligned length for each pair
         let index_alignLen = [];
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
@@ -49914,6 +49914,7 @@ class ChainalignParser {
             // vastplusAtype: 0: VAST, global, 1: VAST, invarant core, 2: TM-align, global
             // VAST+ on the fly
             let structArray = Object.keys(ic.structures);
+            if(vastplusAtype == 2) me.cfg.aligntool = 'tmalign';
             await ic.vastplusCls.vastplusAlign(structArray, vastplusAtype);
         }
 
@@ -55682,7 +55683,8 @@ class ParserUtils {
  
       // display the structure right away. load the mns and sequences later
       setTimeout(async function(){
-          if(ic.bInitial) {
+            if(ic.bInitial) {
+        //   if(!ic.bAnnoShown || ic.bResetAnno) {
             //   if(me.cfg.showsets) {
             //        ic.definedSetsCls.showSets();
             //   }
@@ -57356,7 +57358,14 @@ class SetSeqAlign {
                     //     resi = ic.qt_start_end[chainIndex][i].t_start;
                     // }
                     // else {
-                        let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
+                        // 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;
+                        }
                         resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
                     // }
 
@@ -59150,6 +59159,7 @@ class Vastplus {
         }
 
         let bRealign = true, atype = 2; // VAST+ based on TM-align
+        me.cfg.aligntool = 'tmalign';
         await ic.vastplusCls.vastplusAlign(Object.keys(structHash), atype, bRealign);
     }
 
@@ -60094,7 +60104,7 @@ class ApplyCommand {
       else if(command == 'set annotation ig') {
           ic.bRunRefnumAgain = true;
           await ic.annotationCls.setAnnoTabIg();
-          // ic.bRunRefnumAgain = false;
+          ic.bRunRefnumAgain = false;
       }
       else if(command == 'ig refnum on') {
         ic.bRunRefnumAgain = true;
@@ -60102,7 +60112,7 @@ class ApplyCommand {
         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
         await ic.annotationCls.setAnnoTabIg(true);
 
-        // ic.bRunRefnumAgain = false;
+        ic.bRunRefnumAgain = false;
     }
       else if(command == 'highlight level up') {
           ic.resid2specCls.switchHighlightLevelUp();
@@ -62825,7 +62835,7 @@ class LoadScript {
                         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
                         await ic.annotationCls.setAnnoTabIg(true);
 
-                        // ic.bRunRefnumAgain = false;
+                        ic.bRunRefnumAgain = false;
                     }
                     else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
                         thisClass.applyCommand3ddomain(lastCommand);
@@ -65852,7 +65862,7 @@ class Dssp {
 
     setRefPdbs() { let ic = this.icn3d; ic.icn3dui;
         // round 1, 16 templates
-        ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_Iset', '1CD28_1yjdC_human_V', '1CD19_6al5A_human_C2orV-n1'];
+        ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_C2', '1CD28_1yjdC_human_V', '1CD19_6al5A_human-n1'];
 
         // round 2
         ic.refpdbHash = {};
@@ -65862,19 +65872,19 @@ class Dssp {
         ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
         ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
         ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
-        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
-        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
+        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'VTCN1_Q7Z7D3_human_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C1-n2'];
         ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2'];
         ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
         ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V'];
         ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
-        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'LAG3_7tzgD_human_C2-n2', 'JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2'];
-        ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_Iset'];
-        ic.refpdbHash['1CD3g_6jxrg_human_Iset'] = ['CD3g_6jxrg_human_Iset', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
-        ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_Iset'];
-        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
+        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152', 'LAG3_7tzgD_human_C1-n2', 'JAM1_1nbqA_human_Iset-n2', 'Contactin1_3s97C_human_Iset-n2'];
+        ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_C1'];
+        ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
+        ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_C1'];
+        ic.refpdbHash['1CD19_6al5A_human-n1'] = ['CD19_6al5A_human-n1'];
 
-        ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_Iset', 'CD3e_6jxrf_human_Iset', 'CD3g_6jxrg_human_Iset', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_C2-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_FN3-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C2-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
+        ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'CD3g_6jxrg_human_C2', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_Iset-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_C1-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_Iset-n2', 'LAG3_7tzgD_human_C1-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Iset-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_C1-n2'];
 
         // use known ref structure
         ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -65882,7 +65892,7 @@ class Dssp {
         ic.refpdbHash['8GUY_E'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2'];
         ic.refpdbHash['6JXR_m'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
         ic.refpdbHash['1HNF_A'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
-        ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C2-n2'];
+        ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C1-n2'];
         ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
         ic.refpdbHash['1BQU_B'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
 
@@ -65892,7 +65902,7 @@ class Dssp {
         ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
         ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
         ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
-        ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_VorIset-n2'];
+        ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_Iset-n2'];
         ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
         ic.refpdbHash['7PHR_H'] = ['MHCIa_7phrH_human_C1'];
         ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
@@ -65904,9 +65914,9 @@ class Dssp {
         ic.refpdbHash['2AW2_A'] = ['BTLA_2aw2A_human_Iset'];
         ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
         ic.refpdbHash['1WF5_A'] = ['Sidekick2_1wf5A_human_FN3-n7'];
-        ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C2-n2'];
+        ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C1-n2'];
         ic.refpdbHash['1IFR_A'] = ['LaminAC_1ifrA_human'];
-        ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_V-n2'];
+        ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_C1-n2'];
         ic.refpdbHash['4ZQK_B'] = ['PD1_4zqkB_human_V'];
         ic.refpdbHash['2DM3_A'] = ['Palladin_2dm3A_human_Iset-n1'];
         ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
@@ -65914,17 +65924,17 @@ class Dssp {
         ic.refpdbHash['4ZT1_A'] = ['ECadherin_4zt1A_human_n2'];
         ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
         ic.refpdbHash['1CD8_A'] = ['CD8a_1cd8A_human_V'];
-        ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_C2-n2'];
-        ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_FN3-n1'];
+        ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_Iset-n2'];
+        ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_C1-n1'];
         ic.refpdbHash['6X4G_A'] = ['ICOS_6x4gA_human_V'];
         ic.refpdbHash['2EE2_A'] = ['Contactin1_2ee2A_human_FN3-n9'];
-        ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Unk-n152'];
-        ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human_C2orV-n1'];
+        ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Iset-n152'];
+        ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human-n1'];
         ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
         ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
-        ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_Iset'];
-        ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_Iset'];
-        ic.refpdbHash['6JXR_g'] = ['CD3g_6jxrg_human_Iset'];
+        ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_C1'];
+        ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_C1'];
+        ic.refpdbHash['6JXR_g'] = ['CD3g_6jxrg_human_C2'];
 
         // assign Ig types
         ic.ref2igtype = {};
@@ -65934,17 +65944,17 @@ class Dssp {
         ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
         ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
         ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
-        ic.ref2igtype['CD19_6al5A_human_C2orV-n1'] = 'CD19';
+        ic.ref2igtype['CD19_6al5A_human-n1'] = 'CD19';
         ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
         ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
         ic.ref2igtype['CD2_1hnfA_human_V-n1'] = 'IgV';
-        ic.ref2igtype['CD3d_6jxrd_human_Iset'] = 'IgI';
-        ic.ref2igtype['CD3e_6jxrf_human_Iset'] = 'IgI';
-        ic.ref2igtype['CD3g_6jxrg_human_Iset'] = 'IgI';
+        ic.ref2igtype['CD3d_6jxrd_human_C1'] = 'IgI';
+        ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgI';
+        ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgI';
         ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
         ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
         ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
-        ic.ref2igtype['Contactin1_3s97C_human_C2-n2'] = 'IgC2';
+        ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgC2';
         ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
         ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
         ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
@@ -65952,15 +65962,15 @@ class Dssp {
         ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
         ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
         ic.ref2igtype['FAB-LIGHT_5esv_V-n1'] = 'IgV';
-        ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFN3';
+        ic.ref2igtype['GHR_1axiB_human_C1-n1'] = 'IgFN3';
         ic.ref2igtype['ICOS_6x4gA_human_V'] = 'IgV';
         ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFN3';
         ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
         ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
         ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
         ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
-        ic.ref2igtype['JAM1_1nbqA_human_VorIset-n2'] = 'IgI';
-        ic.ref2igtype['LAG3_7tzgD_human_C2-n2'] = 'IgC2';
+        ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
+        ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC2';
         ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
         ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
         ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
@@ -65974,16 +65984,16 @@ class Dssp {
         ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
         ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
         ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
-        ic.ref2igtype['Siglec3_5j0bB_human_C2-n2'] = 'IgC2';
+        ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC2';
         ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
         ic.ref2igtype['TEAD1_3kysC_human'] = 'IgE';
         ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
         ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
-        ic.ref2igtype['Titin_4uowM_human_Unk-n152'] = 'IgI';
+        ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
         ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
         ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
-        ic.ref2igtype['VTCN1_Q7Z7D3_human_V-n2'] = 'IgV';
+        ic.ref2igtype['VTCN1_Q7Z7D3_human_C1-n2'] = 'IgV';
     }
 
     getPdbAjaxArray() {  let ic = this.icn3d, me = ic.icn3dui;
@@ -66456,8 +66466,6 @@ class Dssp {
             }
         }
 
-        //!!!
-
         // combine the top four clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
@@ -66700,7 +66708,7 @@ class Dssp {
 
             let currStrand;
 
-            // let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
+            // let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human-n1';
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 if(!seg) continue;
@@ -67391,13 +67399,15 @@ class Dssp {
                 if(i != il - 1) { // modify 
                     strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                 }
+                
+                // assign before removing
+                let resid = chnid + '_' + strandArray[i].startResi;
 
                 strandArray.splice(i, 1);
 
                 if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
                     if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
                     
-                    let resid = chnid + '_' + strandArray[i].startResi;
                     let domainid = ic.resid2domainid[resid];
                     removeDomainidHash[domainid] = 1;
                     continue;