diff --git a/src/mol-geo/geometry/color-data.ts b/src/mol-geo/geometry/color-data.ts
index 457c6a14db1e9fdcae82fa889966685f43852537..cc66f80c9edd161b5a518d38acab4be1f9faedc1 100644
--- a/src/mol-geo/geometry/color-data.ts
+++ b/src/mol-geo/geometry/color-data.ts
@@ -37,16 +37,17 @@ export interface ColorProps {
 }
 
 export function getColorThemeProps(props: ColorProps): ColorThemeProps {
-    return {
-        name: props.colorTheme,
-        domain: props.colorDomain,
-        value: props.colorValue,
-        structure: props.structure,
-        color: props.colorFunction,
-        granularity: props.colorGranularity,
-        description: props.colorDescription,
-        legend: props.colorLegend
+    const p: ColorThemeProps = {
+        name: props.colorTheme
     }
+    if (props.colorDomain !== undefined) p.domain = props.colorDomain
+    if (props.colorValue !== undefined) p.value = props.colorValue
+    if (props.structure !== undefined) p.structure = props.structure
+    if (props.colorFunction !== undefined) p.color = props.colorFunction
+    if (props.colorGranularity !== undefined) p.granularity = props.colorGranularity
+    if (props.colorDescription !== undefined) p.description = props.colorDescription
+    if (props.colorLegend !== undefined) p.legend = props.colorLegend
+    return p
 }
 
 export function createColors(ctx: RuntimeContext, locationIt: LocationIterator, props: ColorProps, colorData?: ColorData): Promise<ColorData> {
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index a1822294dcc23c42808cb0fedc553cf43d92360e..d58caef4549e1bb1c98dfff2a1aff0616ee0cd56 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -20,7 +20,7 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
 
 export const StructureParams = {
     ...Geometry.Params,
-    colorTheme: SelectParam<ColorThemeName>('Color Theme', '', 'unit-index', ColorThemeOptions),
+    colorTheme: SelectParam<ColorThemeName>('Color Theme', '', 'polymer-index', ColorThemeOptions),
     sizeTheme: SelectParam<SizeThemeName>('Size Theme', '', 'physical', SizeThemeOptions),
 }
 export const DefaultStructureProps = paramDefaultValues(StructureParams)
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 001b497b62913a702ed8e78df347a929006d922f..c11848731cdae4a30529c7d2e62a9ed272b8cc26 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -22,6 +22,7 @@ import { ResidueNameColorTheme } from './color/residue-name';
 import { SequenceIdColorTheme } from './color/sequence-id';
 import { SecondaryStructureColorTheme } from './color/secondary-structure';
 import { MoleculeTypeColorTheme } from './color/molecule-type';
+import { PolymerIndexColorTheme } from './color/polymer-index';
 
 export type LocationColor = (location: Location, isSecondary: boolean) => Color
 
@@ -59,6 +60,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
         case 'element-index': return ElementIndexColorTheme(props)
         case 'element-symbol': return ElementSymbolColorTheme(props)
         case 'molecule-type': return MoleculeTypeColorTheme(props)
+        case 'polymer-index': return PolymerIndexColorTheme(props)
         case 'residue-name': return ResidueNameColorTheme(props)
         case 'secondary-structure': return SecondaryStructureColorTheme(props)
         case 'sequence-id': return SequenceIdColorTheme(props)
@@ -87,6 +89,7 @@ export const ColorThemeInfo = {
     'element-index': {},
     'element-symbol': {},
     'molecule-type': {},
+    'polymer-index': {},
     'residue-name': {},
     'secondary-structure': {},
     'sequence-id': {},
diff --git a/src/mol-theme/color/polymer-index.ts b/src/mol-theme/color/polymer-index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..891b17300f72f94ab19e1c1883e19c303f9d0659
--- /dev/null
+++ b/src/mol-theme/color/polymer-index.ts
@@ -0,0 +1,53 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorScale, Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { StructureElement, Link } from 'mol-model/structure';
+import { ColorTheme, ColorThemeProps, LocationColor } from '../color';
+
+const DefaultColor = Color(0xCCCCCC)
+const Description = 'Gives every polymer a unique color based on the position (index) of the polymer in the list of polymers in the structure.'
+
+export function PolymerIndexColorTheme(props: ColorThemeProps): ColorTheme {
+    let color: LocationColor
+    let scale: ColorScale | undefined = undefined
+
+    if (props.structure) {
+        const { units } = props.structure
+        let polymerCount = 0
+        for (let i = 0, il = units.length; i <il; ++i) {
+            if (units[i].polymerElements.length > 0) ++polymerCount
+        }
+        scale = ColorScale.create({ domain: [ 0, polymerCount - 1 ] })
+        const unitIdColor = new Map<number, Color>()
+        for (let i = 0, j = 0, il = units.length; i <il; ++i) {
+            if (units[i].polymerElements.length > 0) {
+                unitIdColor.set(units[i].id, scale.color(j))
+                ++j
+            }
+        }
+
+        color = (location: Location): Color => {
+            let color: Color | undefined
+            if (StructureElement.isLocation(location)) {
+                color = unitIdColor.get(location.unit.id)
+            } else if (Link.isLocation(location)) {
+                color = unitIdColor.get(location.aUnit.id)
+            }
+            return color !== undefined ? color : DefaultColor
+        }
+    } else {
+        color = () => DefaultColor
+    }
+
+    return {
+        granularity: 'instance',
+        color,
+        description: Description,
+        legend: scale ? scale.legend : undefined
+    }
+}
\ No newline at end of file
diff --git a/src/mol-theme/color/unit-index.ts b/src/mol-theme/color/unit-index.ts
index 92d4f53bbe552f2017b873dd7778ee0d6621e3e2..3e4fed18b986e43f85fa9c076d9d765695f73494 100644
--- a/src/mol-theme/color/unit-index.ts
+++ b/src/mol-theme/color/unit-index.ts
@@ -21,7 +21,7 @@ export function UnitIndexColorTheme(props: ColorThemeProps): ColorTheme {
         scale = ColorScale.create({ domain: [ 0, units.length - 1 ] })
         const unitIdColor = new Map<number, Color>()
         for (let i = 0, il = units.length; i <il; ++i) {
-            unitIdColor.set(units[i].id, scale.color(units[i].id))
+            unitIdColor.set(units[i].id, scale.color(i))
         }
 
         color = (location: Location): Color => {