Merge branch 'master' into custom-theme-colors

CHANGELOG.md

@@ -16,6 +16,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix coarse model support in entity-id color theme
 - Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
 - Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
+- Support/bugfixes for ``atom_site.pdbx_sifts_xref`` categories
 
 ## [v3.0.0-dev.10] - 2022-01-17
 

package-lock.json

@@ -13,7 +13,7 @@
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         "@types/compression": "1.7.2",
         "@types/express": "^4.17.13",
-        "@types/node": "^16.11.19",
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@@ -26,9 +26,9 @@
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@@ -45,7 +45,7 @@
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+      "integrity": "sha512-x+7e5IqfwLwsxTdliHRtlIYkgdtYXzE0CkFeV6ytAqq431ZyxCFzNMNR5sr3WOlIG/ihVZr9K/y71VHTF/DUQA==",
       "dev": true,
       "requires": {
-        "@typescript-eslint/types": "5.9.1",
-        "@typescript-eslint/visitor-keys": "5.9.1",
+        "@typescript-eslint/types": "5.10.0",
+        "@typescript-eslint/visitor-keys": "5.10.0",
         "debug": "^4.3.2",
         "globby": "^11.0.4",
         "is-glob": "^4.0.3",
@@ -16354,13 +16425,27 @@
         "tsutils": "^3.21.0"
       }
     },
+    "@typescript-eslint/utils": {
+      "version": "5.10.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.10.0.tgz",
+      "integrity": "sha512-IGYwlt1CVcFoE2ueW4/ioEwybR60RAdGeiJX/iDAw0t5w0wK3S7QncDwpmsM70nKgGTuVchEWB8lwZwHqPAWRg==",
+      "dev": true,
+      "requires": {
+        "@types/json-schema": "^7.0.9",
+        "@typescript-eslint/scope-manager": "5.10.0",
+        "@typescript-eslint/types": "5.10.0",
+        "@typescript-eslint/typescript-estree": "5.10.0",
+        "eslint-scope": "^5.1.1",
+        "eslint-utils": "^3.0.0"
+      }
+    },
     "@typescript-eslint/visitor-keys": {
-      "version": "5.9.1",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.9.1.tgz",
-      "integrity": "sha512-Xh37pNz9e9ryW4TVdwiFzmr4hloty8cFj8GTWMXh3Z8swGwyQWeCcNgF0hm6t09iZd6eiZmIf4zHedQVP6TVtg==",
+      "version": "5.10.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.10.0.tgz",
+      "integrity": "sha512-GMxj0K1uyrFLPKASLmZzCuSddmjZVbVj3Ouy5QVuIGKZopxvOr24JsS7gruz6C3GExE01mublZ3mIBOaon9zuQ==",
       "dev": true,
       "requires": {
-        "@typescript-eslint/types": "5.9.1",
+        "@typescript-eslint/types": "5.10.0",
         "eslint-visitor-keys": "^3.0.0"
       }
     },
@@ -17900,20 +17985,12 @@
       "dev": true
     },
     "cross-fetch": {
-      "version": "3.1.4",
-      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.4.tgz",
-      "integrity": "sha512-1eAtFWdIubi6T4XPy6ei9iUFoKpUkIF971QLN8lIvvvwueI65+Nw5haMNKUwfJxabqlIIDODJKGrQ66gxC0PbQ==",
+      "version": "3.1.5",
+      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.5.tgz",
+      "integrity": "sha512-lvb1SBsI0Z7GDwmuid+mU3kWVBwTVUbe7S0H52yaaAdQOXq2YktTCZdlAcNKFzE6QtRz0snpw9bNiPeOIkkQvw==",
       "dev": true,
       "requires": {
-        "node-fetch": "2.6.1"
-      },
-      "dependencies": {
-        "node-fetch": {
-          "version": "2.6.1",
-          "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.1.tgz",
-          "integrity": "sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw==",
-          "dev": true
-        }
+        "node-fetch": "2.6.7"
       }
     },
     "cross-spawn": {
@@ -19119,6 +19196,30 @@
         "mime-types": "^2.1.12"
       }
     },
+    "form-data-encoder": {
+      "version": "1.7.1",
+      "resolved": "https://registry.npmjs.org/form-data-encoder/-/form-data-encoder-1.7.1.tgz",
+      "integrity": "sha512-EFRDrsMm/kyqbTQocNvRXMLjc7Es2Vk+IQFx/YW7hkUH1eBl4J1fqiP34l74Yt0pFLCNpc06fkbVk00008mzjg==",
+      "dev": true
+    },
+    "formdata-node": {
+      "version": "4.3.2",
+      "resolved": "https://registry.npmjs.org/formdata-node/-/formdata-node-4.3.2.tgz",
+      "integrity": "sha512-k7lYJyzDOSL6h917favP8j1L0/wNyylzU+x+1w4p5haGVHNlP58dbpdJhiCUsDbWsa9HwEtLp89obQgXl2e0qg==",
+      "dev": true,
+      "requires": {
+        "node-domexception": "1.0.0",
+        "web-streams-polyfill": "4.0.0-beta.1"
+      },
+      "dependencies": {
+        "web-streams-polyfill": {
+          "version": "4.0.0-beta.1",
+          "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-4.0.0-beta.1.tgz",
+          "integrity": "sha512-3ux37gEX670UUphBF9AMCq8XM6iQ8Ac6A+DSRRjDoRBm1ufCkaCDdNVbaqq60PsEkdNlLKrGtv/YBP4EJXqNtQ==",
+          "dev": true
+        }
+      }
+    },
     "forwarded": {
       "version": "0.2.0",
       "resolved": "https://registry.npmjs.org/forwarded/-/forwarded-0.2.0.tgz",
@@ -21671,9 +21772,9 @@
       "dev": true
     },
     "mini-css-extract-plugin": {
-      "version": "2.4.7",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.4.7.tgz",
-      "integrity": "sha512-euWmddf0sk9Nv1O0gfeeUAvAkoSlWncNLF77C0TP2+WoPvy8mAHKOzMajcCz2dzvyt3CNgxb1obIEVFIRxaipg==",
+      "version": "2.5.2",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.5.2.tgz",
+      "integrity": "sha512-Lwgq9qLNyBK6yNLgzssXnq4r2+mB9Mz3cJWlM8kseysHIvTicFhDNimFgY94jjqlwhNzLPsq8wv4X+vOHtMdYA==",
       "dev": true,
       "requires": {
         "schema-utils": "^4.0.0"
@@ -21851,9 +21952,9 @@
       "optional": true
     },
     "nanoid": {
-      "version": "3.1.30",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.30.tgz",
-      "integrity": "sha512-zJpuPDwOv8D2zq2WRoMe1HsfZthVewpel9CAvTfc/2mBD1uUT/agc5f7GHGWXlYkFvi1mVxe4IjvP2HNrop7nQ==",
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.2.0.tgz",
+      "integrity": "sha512-fmsZYa9lpn69Ad5eDn7FMcnnSR+8R34W9qJEijxYhTbfOWzr22n1QxCMzXLK+ODyW2973V3Fux959iQoUxzUIA==",
       "dev": true
     },
     "napi-build-utils": {
@@ -21898,10 +21999,16 @@
         "semver": "^7.3.5"
       }
     },
+    "node-domexception": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/node-domexception/-/node-domexception-1.0.0.tgz",
+      "integrity": "sha512-/jKZoMpw0F8GRwl4/eLROPA3cfcXtLApP0QzLmUT/HuPCZWyB7IY9ZrMeKw2O/nFIqPQB3PVM9aYm0F312AXDQ==",
+      "dev": true
+    },
     "node-fetch": {
-      "version": "2.6.6",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.6.tgz",
-      "integrity": "sha512-Z8/6vRlTUChSdIgMa51jxQ4lrw/Jy5SOW10ObaA47/RElsAN2c5Pn8bTgFGWn/ibwzXTE8qwr1Yzx28vsecXEA==",
+      "version": "2.6.7",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
+      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
       "requires": {
         "whatwg-url": "^5.0.0"
       },
@@ -23079,9 +23186,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sass": {
-      "version": "1.48.0",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.48.0.tgz",
-      "integrity": "sha512-hQi5g4DcfjcipotoHZ80l7GNJHGqQS5LwMBjVYB/TaT0vcSSpbgM8Ad7cgfsB2M0MinbkEQQPO9+sjjSiwxqmw==",
+      "version": "1.49.0",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.49.0.tgz",
+      "integrity": "sha512-TVwVdNDj6p6b4QymJtNtRS2YtLJ/CqZriGg0eIAbAKMlN8Xy6kbv33FsEZSF7FufFFM705SQviHjjThfaQ4VNw==",
       "dev": true,
       "requires": {
         "chokidar": ">=3.0.0 <4.0.0",
@@ -23646,9 +23753,9 @@
       }
     },
     "swagger-ui-dist": {
-      "version": "4.1.3",
-      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.3.tgz",
-      "integrity": "sha512-WvfPSfAAMlE/sKS6YkW47nX/hA7StmhYnAHc6wWCXNL0oclwLj6UXv0hQCkLnDgvebi0MEV40SJJpVjKUgH1IQ=="
+      "version": "4.2.1",
+      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.2.1.tgz",
+      "integrity": "sha512-ZzUeNKIIMXmKI53iLscAVCpQ7jblYxI2XX5EBaoBr6UBEfxT3L0vlnE+fzPBbHc9g0sgdOMLZGhC5OW++9pqlw=="
     },
     "swap-case": {
       "version": "2.0.2",
@@ -24057,9 +24164,9 @@
       }
     },
     "typescript": {
-      "version": "4.5.4",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.4.tgz",
-      "integrity": "sha512-VgYs2A2QIRuGphtzFV7aQJduJ2gyfTljngLzjpfW9FoYZF6xuw1W0vW9ghCKLfcWrCFxK81CSGRAvS1pn4fIUg==",
+      "version": "4.5.5",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
+      "integrity": "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA==",
       "dev": true
     },
     "ua-parser-js": {
@@ -24308,6 +24415,12 @@
         "defaults": "^1.0.3"
       }
     },
+    "web-streams-polyfill": {
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.0.tgz",
+      "integrity": "sha512-EqPmREeOzttaLRm5HS7io98goBgZ7IVz79aDvqjD0kYXLtFZTc0T/U6wHTPKyIjb+MdN7DFIIX6hgdBEpWmfPA==",
+      "dev": true
+    },
     "webidl-conversions": {
       "version": "6.1.0",
       "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz",
@@ -24315,9 +24428,9 @@
       "dev": true
     },
     "webpack": {
-      "version": "5.66.0",
-      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.66.0.tgz",
-      "integrity": "sha512-NJNtGT7IKpGzdW7Iwpn/09OXz9inIkeIQ/ibY6B+MdV1x6+uReqz/5z1L89ezWnpPDWpXF0TY5PCYKQdWVn8Vg==",
+      "version": "5.67.0",
+      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.67.0.tgz",
+      "integrity": "sha512-LjFbfMh89xBDpUMgA1W9Ur6Rn/gnr2Cq1jjHFPo4v6a79/ypznSYbAyPgGhwsxBtMIaEmDD1oJoA7BEYw/Fbrw==",
       "dev": true,
       "requires": {
         "@types/eslint-scope": "^3.7.0",
@@ -24343,7 +24456,7 @@
         "tapable": "^2.1.1",
         "terser-webpack-plugin": "^5.1.3",
         "watchpack": "^2.3.1",
-        "webpack-sources": "^3.2.2"
+        "webpack-sources": "^3.2.3"
       },
       "dependencies": {
         "acorn-import-assertions": {
@@ -24397,9 +24510,9 @@
       }
     },
     "webpack-sources": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.2.tgz",
-      "integrity": "sha512-cp5qdmHnu5T8wRg2G3vZZHoJPN14aqQ89SyQ11NpGH5zEMDCclt49rzo+MaRazk7/UeILhAI+/sEtcM+7Fr0nw==",
+      "version": "3.2.3",
+      "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
+      "integrity": "sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==",
       "dev": true
     },
     "whatwg-encoding": {
@@ -24512,9 +24625,9 @@
       }
     },
     "ws": {
-      "version": "8.2.3",
-      "resolved": "https://registry.npmjs.org/ws/-/ws-8.2.3.tgz",
-      "integrity": "sha512-wBuoj1BDpC6ZQ1B7DWQBYVLphPWkm8i9Y0/3YdHjHKHiohOJ1ws+3OccDWtH+PoC9DZD5WOTrJvNbWvjS6JWaA==",
+      "version": "8.4.2",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.4.2.tgz",
+      "integrity": "sha512-Kbk4Nxyq7/ZWqr/tarI9yIt/+iNNFOjBXEWgTb4ydaNHBNGgvf2QHbS9fdfsndfjFlFwEd4Al+mw83YkaD10ZA==",
       "dev": true,
       "requires": {}
     },

package.json

@@ -92,7 +92,7 @@
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.3.1",
+    "@graphql-codegen/cli": "^2.4.0",
     "@graphql-codegen/time": "^3.1.1",
     "@graphql-codegen/typescript": "^2.4.2",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
@@ -101,8 +101,8 @@
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
     "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.9.1",
-    "@typescript-eslint/parser": "^5.9.1",
+    "@typescript-eslint/eslint-plugin": "^5.10.0",
+    "@typescript-eslint/parser": "^5.10.0",
     "benchmark": "^2.1.4",
     "concurrently": "^7.0.0",
     "cpx2": "^4.1.2",
@@ -115,17 +115,17 @@
     "graphql": "^16.2.0",
     "http-server": "^14.1.0",
     "jest": "^27.4.7",
-    "mini-css-extract-plugin": "~2.4.7",
+    "mini-css-extract-plugin": "^2.5.2",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.48.0",
+    "sass": "^1.49.0",
     "sass-loader": "^12.4.0",
     "simple-git": "^2.48.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
     "ts-jest": "^27.1.3",
-    "typescript": "^4.5.4",
-    "webpack": "^5.66.0",
+    "typescript": "^4.5.5",
+    "webpack": "^5.67.0",
     "webpack-cli": "^4.9.1"
   },
   "dependencies": {
@@ -133,7 +133,7 @@
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.19",
+    "@types/node": "^16.11.21",
     "@types/node-fetch": "^2.5.12",
     "@types/react": "^17.0.38",
     "@types/react-dom": "^17.0.11",
@@ -146,9 +146,9 @@
     "h264-mp4-encoder": "^1.0.12",
     "immer": "^9.0.12",
     "immutable": "^4.0.0",
-    "node-fetch": "^2.6.2",
+    "node-fetch": "^2.6.7",
     "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.1.3",
+    "swagger-ui-dist": "^4.2.1",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"

src/apps/viewer/app.ts

@@ -101,7 +101,14 @@ export class Viewer {
     }
 
     static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
         const defaultSpec = DefaultPluginUISpec();
 
         const spec: PluginUISpec = {

src/apps/viewer/index.html

@@ -57,7 +57,7 @@
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -71,7 +71,7 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
                 preferWebgl1: preferWebgl1,
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();

src/extensions/model-export/export.ts

@@ -5,7 +5,7 @@
  */
 
 import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
-import { to_mmCIF } from '../../mol-model/structure';
+import { to_mmCIF, Unit } from '../../mol-model/structure';
 import { PluginContext } from '../../mol-plugin/context';
 import { Task } from '../../mol-task';
 import { getFormattedTime } from '../../mol-util/date';
@@ -38,6 +38,10 @@ function _exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'b
                 plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
                 continue;
             }
+            if (s.units.some(u => !Unit.isAtomic(u))) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
+                continue;
+            }
 
             const name = entryMap.has(s.model.entryId)
                 ? `${s.model.entryId}_${entryMap.get(s.model.entryId)! + 1}.${format}`

src/mol-model-props/sequence/best-database-mapping.ts

@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
@@ -40,7 +40,7 @@ namespace BestDatabaseSequenceMapping {
         const data = Provider.get(model).value;
         if (!data) return '';
         const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         return data.accession[rI];
     }
 
@@ -49,7 +49,7 @@ namespace BestDatabaseSequenceMapping {
         const data = Provider.get(model).value;
         if (!data) return;
         const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         const dbName = data.dbName[rI];
         if (!dbName) return;
         return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
@@ -59,10 +59,10 @@ namespace BestDatabaseSequenceMapping {
         if (!MmcifFormat.is(model.sourceData)) return;
 
         const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('db_name');
-        const db_acc = atom_site.getField('db_acc');
-        const db_num = atom_site.getField('db_num');
-        const db_res = atom_site.getField('db_res');
+        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
+        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
+        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
+        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');
 
         if (!db_name || !db_acc || !db_num || !db_res) return;
 
@@ -77,17 +77,17 @@ namespace BestDatabaseSequenceMapping {
             const row = atomSourceIndex.value(residueOffsets[i]);
 
             if (db_name.valueKind(row) !== Column.ValueKind.Present) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = 0;
+                residue[i] = '';
                 continue;
             }
 
-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = db_res.str(row);
+            dbName[i] = db_name.str(row);
+            accession[i] = db_acc.str(row);
+            num[i] = db_num.int(row);
+            residue[i] = db_res.str(row);
         }
 
         return { dbName, accession, num, residue };

src/mol-model/structure/structure/util/superposition-db-mapping.ts

@@ -5,6 +5,7 @@
  */
 
 import { Segmentation } from '../../../../mol-data/int';
+import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
 import { ElementIndex } from '../../model/indexing';
@@ -33,6 +34,7 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
     for (const p of pairs) {
         const [a, b] = getPositionTables(index, p.i, p.j, p.count);
         const transform = MinimizeRmsd.compute({ a, b });
+        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
         ret.push({ transform, pivot: p.i, other: p.j });
     }
 
@@ -51,6 +53,8 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:
 
         const l = Math.min(a[2] - a[1], b[2] - b[1]);
 
+        // TODO: allow to use just backbone atoms?
+        // TODO: check if residue types match?
         for (let i = 0; i < l; i++) {
             let eI = (a[1] + i) as ElementIndex;
             xs.x[o] = a[0].conformation.x(eI);
@@ -122,7 +126,6 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
         if (unit.kind !== Unit.Kind.Atomic) continue;
 
         const { elements, model } = unit;
-        const { offsets: residueOffset } = model.atomicHierarchy.residueAtomSegments;
 
         const map = BestDatabaseSequenceMapping.Provider.get(model).value;
         if (!map) return;
@@ -137,23 +140,27 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
             residuesIt.setSegment(chainSegment);
             while (residuesIt.hasNext) {
                 const residueSegment = residuesIt.move();
-                const eI = elements[residueSegment.start];
-                const rI = residueOffset[eI];
+                const rI = residueSegment.index;
 
                 if (!dbName[rI]) continue;
 
+                const start = elements[residueSegment.start];
+                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+
                 const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;
 
                 if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, eI, elements[residueSegment.end]] } });
+                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
                 } else {
                     const entry = index.get(key)!;
 
                     if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, eI, elements[residueSegment.end]];
+                        entry.pivots[sI] = [unit, start, end];
                     }
                 }
             }
         }
     }
+
+    console.log(index);
 }

src/mol-plugin-ui/structure/superposition.tsx

@@ -185,9 +185,9 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             rmsd += xform.transform.rmsd;
         }
 
-        rmsd /= transforms.length - 1;
+        rmsd /= Math.max(transforms.length - 1, 1);
 
-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)}.`);
+        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
         await new Promise(res => requestAnimationFrame(res));
         PluginCommands.Camera.Reset(this.plugin);
     };