diff --git a/package.json b/package.json
index f0346afd0..6404b580f 100644
--- a/package.json
+++ b/package.json
@@ -8,7 +8,7 @@
     "build:webpack": "cross-env NODE_ENV=production webpack --config webpack.config.prod.js --progress",
     "build:analyze": "cross-env NODE_ENV=production webpack --config webpack.config.prod.js --json | webpack-bundle-size-analyzer",
     "build": "npm run clean && npm run build:webpack",
-    "start": "cross-env NODE_ENV=development DEBUG=1 ./node_modules/.bin/nodemon --watch server index.js",
+    "start": "cross-env NODE_ENV=development DEBUG=sql ./node_modules/.bin/nodemon --watch server index.js",
     "lint": "eslint frontend",
     "deploy": "git push heroku master",
     "heroku-postbuild": "npm run build && npm run sequelize db:migrate",
diff --git a/server/api/documents.js b/server/api/documents.js
index f0366477f..c8fa8f21d 100644
--- a/server/api/documents.js
+++ b/server/api/documents.js
@@ -52,7 +52,8 @@ router.post('documents.search', auth(), async (ctx) => {
   const sql = `
   SELECT * FROM documents
   WHERE "searchVector" @@ plainto_tsquery('english', :query) AND
-    "teamId" = '${user.teamId}'::uuid
+    "teamId" = '${user.teamId}'::uuid AND
+    "deletedAt" IS NULL
   ORDER BY ts_rank(documents."searchVector", plainto_tsquery('english', :query))
   DESC;
   `;
@@ -199,12 +200,13 @@ router.post('documents.delete', auth(), async (ctx) => {
     } catch (e) {
       throw httpErrors.BadRequest('Error while deleting');
     }
-  } else {
-    try {
-      await document.destroy();
-    } catch (e) {
-      throw httpErrors.BadRequest('Error while deleting');
-    }
+  }
+
+  // Delete the actual document
+  try {
+    await document.destroy();
+  } catch (e) {
+    throw httpErrors.BadRequest('Error while deleting document');
   }
 
   ctx.body = {
diff --git a/server/migrations/20160726061511-atlas-creator.js b/server/migrations/20160726061511-atlas-creator.js
index d8afeda71..1d6285863 100644
--- a/server/migrations/20160726061511-atlas-creator.js
+++ b/server/migrations/20160726061511-atlas-creator.js
@@ -13,6 +13,6 @@ module.exports = {
   },
 
   down: function (queryInterface, Sequelize) {
-    queryInterface.removeColumn('documents', 'creatorId');
+    queryInterface.removeColumn('atlases', 'creatorId');
   }
 };
diff --git a/server/migrations/20160812145029-document-atlas-soft-delete.js b/server/migrations/20160812145029-document-atlas-soft-delete.js
new file mode 100644
index 000000000..a2081fc46
--- /dev/null
+++ b/server/migrations/20160812145029-document-atlas-soft-delete.js
@@ -0,0 +1,28 @@
+'use strict';
+
+module.exports = {
+  up: function (queryInterface, Sequelize) {
+    queryInterface.addColumn(
+      'atlases',
+      'deletedAt',
+      {
+        type: Sequelize.DATE,
+        allowNull: true,
+      }
+    );
+
+    queryInterface.addColumn(
+      'documents',
+      'deletedAt',
+      {
+        type: Sequelize.DATE,
+        allowNull: true,
+      }
+    );
+  },
+
+  down: function (queryInterface, Sequelize) {
+    queryInterface.removeColumn('atlases', 'deletedAt');
+    queryInterface.removeColumn('documents', 'deletedAt');
+  }
+};
diff --git a/server/migrations/20160814083127-paranoia-indeces.js b/server/migrations/20160814083127-paranoia-indeces.js
new file mode 100644
index 000000000..b488d56f3
--- /dev/null
+++ b/server/migrations/20160814083127-paranoia-indeces.js
@@ -0,0 +1,41 @@
+'use strict';
+
+module.exports = {
+  up: function (queryInterface, Sequelize) {
+    // Remove old indeces
+    queryInterface.removeIndex('documents', ['urlId']);
+    queryInterface.removeIndex('documents', ['id', 'atlasId']);
+    queryInterface.removeIndex('documents', ['id', 'teamId']);
+    queryInterface.removeIndex('documents', ['parentDocumentId', 'atlasId']);
+
+    queryInterface.removeIndex('atlases', ['id', 'teamId']);
+
+    // Add new ones
+    queryInterface.addIndex('documents', ['id', 'deletedAt']);
+    queryInterface.addIndex('documents', ['urlId', 'deletedAt']);
+    queryInterface.addIndex('documents', ['id', 'atlasId', 'deletedAt']);
+    queryInterface.addIndex('documents', ['id', 'teamId', 'deletedAt']);
+    queryInterface.addIndex('documents', ['parentDocumentId', 'atlasId', 'deletedAt']);
+
+    queryInterface.addIndex('atlases', ['id', 'deletedAt']);
+    queryInterface.addIndex('atlases', ['id', 'teamId', 'deletedAt']);
+  },
+
+  down: function (queryInterface, Sequelize) {
+    queryInterface.addIndex('documents', ['urlId']);
+    queryInterface.addIndex('documents', ['id', 'atlasId']);
+    queryInterface.addIndex('documents', ['id', 'teamId']);
+    queryInterface.addIndex('documents', ['parentDocumentId', 'atlasId']);
+
+    queryInterface.addIndex('atlases', ['id', 'teamId']);
+
+    queryInterface.removeIndex('documents', ['id', 'deletedAt']);
+    queryInterface.removeIndex('documents', ['urlId', 'deletedAt']);
+    queryInterface.removeIndex('documents', ['id', 'atlasId', 'deletedAt']);
+    queryInterface.removeIndex('documents', ['id', 'teamId', 'deletedAt']);
+    queryInterface.removeIndex('documents', ['parentDocumentId', 'atlasId', 'deletedAt']);
+
+    queryInterface.removeIndex('atlases', ['id', 'deletedAt']);
+    queryInterface.removeIndex('atlases', ['id', 'teamId', 'deletedAt']);
+  }
+};
diff --git a/server/models/Atlas.js b/server/models/Atlas.js
index c20b6b407..bf717105c 100644
--- a/server/models/Atlas.js
+++ b/server/models/Atlas.js
@@ -18,26 +18,28 @@ const Atlas = sequelize.define('atlas', {
   navigationTree: DataTypes.JSONB,
 }, {
   tableName: 'atlases',
+  paranoid: true,
   hooks: {
-    afterCreate: async (atlas) => {
-      if (atlas.type !== 'atlas') return;
+    afterCreate: async (collection) => {
+      if (collection.type !== 'atlas') return;
 
       await Document.create({
         parentDocumentId: null,
-        atlasId: atlas.id,
-        teamId: atlas.teamId,
-        userId: atlas.creatorId,
-        lastModifiedById: atlas.creatorId,
+        atlasId: collection.id,
+        teamId: collection.teamId,
+        userId: collection.creatorId,
+        lastModifiedById: collection.creatorId,
         title: 'Introduction',
         text: '# Introduction',
       });
+      await collection.buildStructure();
+      await collection.save();
     },
   },
   instanceMethods: {
-    async getStructure() {
-      if (this.navigationTree) {
-        return this.navigationTree;
-      }
+    async buildStructure() {
+      console.log('start');
+      if (this.navigationTree) return this.navigationTree;
 
       const getNodeForDocument = async (document) => {
         const children = await Document.findAll({ where: {
@@ -47,7 +49,7 @@ const Atlas = sequelize.define('atlas', {
 
         const childNodes = [];
         await Promise.all(children.map(async (child) => {
-          childNodes.push(await getNodeForDocument(child));
+          return childNodes.push(await getNodeForDocument(child));
         }));
 
         return {
@@ -65,11 +67,8 @@ const Atlas = sequelize.define('atlas', {
         },
       });
 
-      if (rootDocument) {
-        return await getNodeForDocument(rootDocument);
-      } else {
-        return true; // TODO should create a root doc
-      }
+      this.navigationTree = await getNodeForDocument(rootDocument);
+      return this.navigationTree;
     },
     async updateNavigationTree(tree = this.navigationTree) {
       const nodeIds = [];
diff --git a/server/models/Document.js b/server/models/Document.js
index 8570dde94..60ce96eda 100644
--- a/server/models/Document.js
+++ b/server/models/Document.js
@@ -58,6 +58,7 @@ const Document = sequelize.define('document', {
     },
   },
 }, {
+  paranoid: true,
   hooks: {
     beforeValidate: (doc) => {
       doc.urlId = randomstring.generate(15);
diff --git a/server/presenters.js b/server/presenters.js
index 6c6b80fde..da98ea6f2 100644
--- a/server/presenters.js
+++ b/server/presenters.js
@@ -59,9 +59,7 @@ export function presentCollection(collection, includeRecentDocuments=false) {
       type: collection.type,
     };
 
-    if (collection.type === 'atlas') {
-      data.navigationTree = await collection.getStructure();
-    }
+    if (collection.type === 'atlas') data.navigationTree = collection.navigationTree;
 
     if (includeRecentDocuments) {
       const documents = await Document.findAll({