diff --git a/services/web/app/coffee/Features/Compile/ClsiManager.coffee b/services/web/app/coffee/Features/Compile/ClsiManager.coffee
old mode 100644
new mode 100755
index b7930f5cf3..639511154e
--- a/services/web/app/coffee/Features/Compile/ClsiManager.coffee
+++ b/services/web/app/coffee/Features/Compile/ClsiManager.coffee
@@ -8,8 +8,8 @@ logger = require "logger-sharelatex"
 url = require("url")
 
 module.exports = ClsiManager =
-	sendRequest: (project_id, callback = (error, success) ->) ->
-		ClsiManager._buildRequest project_id, (error, req) ->
+	sendRequest: (project_id, settingsOverride = {}, callback = (error, success) ->) ->
+		ClsiManager._buildRequest project_id, settingsOverride, (error, req) ->
 			return callback(error) if error?
 			logger.log project_id: project_id, "sending compile to CLSI"
 			ClsiManager._postToClsi project_id, req, (error, response) ->
@@ -52,7 +52,7 @@ module.exports = ClsiManager =
 		return outputFiles
 
 	VALID_COMPILERS: ["pdflatex", "latex", "xelatex", "lualatex"]
-	_buildRequest: (project_id, callback = (error, request) ->) ->
+	_buildRequest: (project_id, settingsOverride={}, callback = (error, request) ->) ->
 		Project.findById project_id, {compiler: 1, rootDoc_id: 1}, (error, project) ->
 			return callback(error) if error?
 			return callback(new Errors.NotFoundError("project does not exist: #{project_id}")) if !project?
@@ -67,6 +67,7 @@ module.exports = ClsiManager =
 
 					resources = []
 					rootResourcePath = null
+					rootResourcePathOverride = null
 
 					for path, doc of docs
 						path = path.replace(/^\//, "") # Remove leading /
@@ -75,6 +76,10 @@ module.exports = ClsiManager =
 							content: doc.lines.join("\n")
 						if project.rootDoc_id? and doc._id.toString() == project.rootDoc_id.toString()
 							rootResourcePath = path
+						if settingsOverride.rootDoc_id? and doc._id.toString() == settingsOverride.rootDoc_id.toString()
+							rootResourcePathOverride = path
+
+					rootResourcePath = rootResourcePathOverride if rootResourcePathOverride?
 
 					for path, file of files
 						path = path.replace(/^\//, "") # Remove leading /
diff --git a/services/web/app/coffee/Features/Compile/CompileController.coffee b/services/web/app/coffee/Features/Compile/CompileController.coffee
old mode 100644
new mode 100755
index aa4fab9e30..0d919fbd75
--- a/services/web/app/coffee/Features/Compile/CompileController.coffee
+++ b/services/web/app/coffee/Features/Compile/CompileController.coffee
@@ -11,9 +11,11 @@ module.exports = CompileController =
 	compile: (req, res, next = (error) ->) ->
 		project_id = req.params.Project_id
 		isAutoCompile = !!req.query?.auto_compile
+		settingsOverride = req.body?.settingsOverride ? {};
+		logger.log "root doc overriden" if settingsOverride.rootDoc_id?
 		AuthenticationController.getLoggedInUserId req, (error, user_id) ->
 			return next(error) if error?
-			CompileManager.compile project_id, user_id, { isAutoCompile }, (error, status, outputFiles) ->
+			CompileManager.compile project_id, user_id, { isAutoCompile, settingsOverride }, (error, status, outputFiles) ->
 				return next(error) if error?
 				res.contentType("application/json")
 				res.send 200, JSON.stringify {
diff --git a/services/web/app/coffee/Features/Compile/CompileManager.coffee b/services/web/app/coffee/Features/Compile/CompileManager.coffee
old mode 100644
new mode 100755
index a0b242e95f..972b7d3286
--- a/services/web/app/coffee/Features/Compile/CompileManager.coffee
+++ b/services/web/app/coffee/Features/Compile/CompileManager.coffee
@@ -25,12 +25,12 @@ module.exports = CompileManager =
 				return callback(error) if error?
 				if recentlyCompiled
 					return callback new Error("project was recently compiled so not continuing")
-
+				
 				CompileManager._ensureRootDocumentIsSet project_id, (error) ->
 					return callback(error) if error?
 					DocumentUpdaterHandler.flushProjectToMongo project_id, (error) ->
 						return callback(error) if error?
-						ClsiManager.sendRequest project_id, (error, status, outputFiles) ->
+						ClsiManager.sendRequest project_id, opt.settingsOverride, (error, status, outputFiles) ->
 							return callback(error) if error?
 							logger.log files: outputFiles, "output files"
 							callback(null, status, outputFiles)
diff --git a/services/web/public/coffee/pdf/CompiledView.coffee b/services/web/public/coffee/pdf/CompiledView.coffee
old mode 100644
new mode 100755
index 4f12007379..74afc1e11b
--- a/services/web/public/coffee/pdf/CompiledView.coffee
+++ b/services/web/public/coffee/pdf/CompiledView.coffee
@@ -204,7 +204,12 @@ define [
 
 		recompilePdf: () ->
 			@options.manager.trigger "compile:pdf"
-			@options.manager.refreshPdf()
+			rootDocOverride_id = null
+			for line in @ide.editor.getLines()
+				match = line.match /(.*)\\documentclass/
+				if match and !match[1].match /%/
+					rootDocOverride_id = @ide.editor.getCurrentDocId()
+			@options.manager.refreshPdf {rootDocOverride_id}
 
 		toggleFlatViewButton: () -> @$("#flatViewButton").button("toggle")
 		toggleSplitViewButton: () -> @$("#splitViewButton").button("toggle")
diff --git a/services/web/public/coffee/pdf/PdfManager.coffee b/services/web/public/coffee/pdf/PdfManager.coffee
index 04bb682bf9..d988797904 100644
--- a/services/web/public/coffee/pdf/PdfManager.coffee
+++ b/services/web/public/coffee/pdf/PdfManager.coffee
@@ -143,7 +143,7 @@ define [
 				@view.onCompiling()
 				@syncButtonsView?.hide()
 				@compiling = true
-				@_doCompile opts.isAutoCompile, (error, status, outputFiles) =>
+				@_doCompile opts, (error, status, outputFiles) =>
 					@compiling = false
 					doneCompiling()
 
@@ -172,16 +172,19 @@ define [
 					if outputFiles?
 						@view.showOutputFileDownloadLinks(outputFiles)
 
-		_doCompile: (isAutoCompile, callback = (error, status, outputFiles) ->) ->
+		_doCompile: (opts, callback = (error, status, outputFiles) ->) ->
 			url = "/project/#{@ide.project_id}/compile"
-			if isAutoCompile
+			if opts.isAutoCompile
 				url += "?auto_compile=true"
 			$.ajax(
 				url: url
 				type: "POST"
 				headers:
 					"X-CSRF-Token": window.csrfToken
+				contentType: "application/json; charset=utf-8"
 				dataType: 'json'
+				data: JSON.stringify settingsOverride: 
+					rootDoc_id: opts.rootDocOverride_id ? null
 				success: (body, status, response) ->
 					callback null, body.status, body.outputFiles
 				error: (error) ->
diff --git a/services/web/test/UnitTests/coffee/Compile/ClsiManagerTests.coffee b/services/web/test/UnitTests/coffee/Compile/ClsiManagerTests.coffee
index 6791443c9a..6915529b95 100644
--- a/services/web/test/UnitTests/coffee/Compile/ClsiManagerTests.coffee
+++ b/services/web/test/UnitTests/coffee/Compile/ClsiManagerTests.coffee
@@ -24,7 +24,7 @@ describe "ClsiManager", ->
 
 	describe "sendRequest", ->
 		beforeEach ->
-			@ClsiManager._buildRequest = sinon.stub().callsArgWith(1, null, @request = "mock-request")
+			@ClsiManager._buildRequest = sinon.stub().callsArgWith(2, null, @request = "mock-request")
 
 		describe "with a successful compile", ->
 			beforeEach ->
@@ -39,7 +39,7 @@ describe "ClsiManager", ->
 							type: "log"
 						}]
 				})
-				@ClsiManager.sendRequest @project_id, @callback
+				@ClsiManager.sendRequest @project_id, {}, @callback
 
 			it "should build the request", ->
 				@ClsiManager._buildRequest
@@ -67,7 +67,7 @@ describe "ClsiManager", ->
 					compile:
 						status: @status = "failure"
 				})
-				@ClsiManager.sendRequest @project_id, @callback
+				@ClsiManager.sendRequest @project_id, {}, @callback
 			
 			it "should call the callback with a failure statue", ->
 				@callback.calledWith(null, @status).should.equal true
@@ -121,7 +121,7 @@ describe "ClsiManager", ->
 
 		describe "with a valid project", ->
 			beforeEach (done) ->
-				@ClsiManager._buildRequest @project_id, (error, request) =>
+				@ClsiManager._buildRequest @project_id, null, (error, request) =>
 					@request = request
 					done()
 
@@ -159,10 +159,32 @@ describe "ClsiManager", ->
 						}]
 				)
 
+
+		describe "when root doc override is valid", ->
+			beforeEach (done) ->
+				@ClsiManager._buildRequest @project_id, {rootDoc_id:"mock-doc-id-2"}, (error, request) =>
+					@request = request
+					done()
+
+			it "should change root path", ->
+				@request.compile.rootResourcePath.should.equal "chapters/chapter1.tex"
+
+
+		describe "when root doc override is invalid", ->
+			beforeEach (done) ->
+				@ClsiManager._buildRequest @project_id, {rootDoc_id:"invalid-id"}, (error, request) =>
+					@request = request
+					done()
+
+			it "should fallback to default root doc", ->
+				@request.compile.rootResourcePath.should.equal "main.tex"
+
+
+
 		describe "when the project has an invalid compiler", ->
 			beforeEach (done) ->
 				@project.compiler = "context"
-				@ClsiManager._buildRequest @project, (error, request) =>
+				@ClsiManager._buildRequest @project, null, (error, request) =>
 					@request = request
 					done()
 
@@ -172,7 +194,7 @@ describe "ClsiManager", ->
 		describe "when there is no valid root document", ->
 			beforeEach (done) ->
 				@project.rootDoc_id = "not-valid"
-				@ClsiManager._buildRequest @project, (@error, @request) =>
+				@ClsiManager._buildRequest @project, null, (@error, @request) =>
 					done()
 			
 			it "should return an error", ->
diff --git a/services/web/test/UnitTests/coffee/Compile/CompileControllerTests.coffee b/services/web/test/UnitTests/coffee/Compile/CompileControllerTests.coffee
index 0820c0431c..fe456995ad 100644
--- a/services/web/test/UnitTests/coffee/Compile/CompileControllerTests.coffee
+++ b/services/web/test/UnitTests/coffee/Compile/CompileControllerTests.coffee
@@ -44,7 +44,7 @@ describe "CompileController", ->
 
 			it "should do the compile without the auto compile flag", ->
 				@CompileManager.compile
-					.calledWith(@project_id, @user_id, { isAutoCompile: false })
+					.calledWith(@project_id, @user_id, { isAutoCompile: false, settingsOverride:{} })
 					.should.equal true
 
 			it "should set the content-type of the response to application/json", ->
@@ -71,7 +71,7 @@ describe "CompileController", ->
 
 			it "should do the compile with the auto compile flag", ->
 				@CompileManager.compile
-					.calledWith(@project_id, @user_id, { isAutoCompile: true })
+					.calledWith(@project_id, @user_id, { isAutoCompile: true, settingsOverride:{} })
 					.should.equal true
 
 	describe "downloadPdf", ->
diff --git a/services/web/test/UnitTests/coffee/Compile/CompileManagerTests.coffee b/services/web/test/UnitTests/coffee/Compile/CompileManagerTests.coffee
index f1b963a8c5..c284341bf2 100644
--- a/services/web/test/UnitTests/coffee/Compile/CompileManagerTests.coffee
+++ b/services/web/test/UnitTests/coffee/Compile/CompileManagerTests.coffee
@@ -36,7 +36,7 @@ describe "CompileManager", ->
 			@CompileManager._checkIfRecentlyCompiled = sinon.stub().callsArgWith(2, null, false)
 			@CompileManager._ensureRootDocumentIsSet = sinon.stub().callsArgWith(1, null)
 			@DocumentUpdaterHandler.flushProjectToMongo = sinon.stub().callsArgWith(1, null)
-			@ClsiManager.sendRequest = sinon.stub().callsArgWith(1, null, @status = "mock-status")
+			@ClsiManager.sendRequest = sinon.stub().callsArgWith(2, null, @status = "mock-status")
 
 		describe "succesfully", ->
 			beforeEach ->