Color management and CMYK color space

CueMol (after version supports the color management using the ICC color profile files. This feature enable you to create the molecular images suitable for the specific output devices and color spaces (e.g., CMYK color space). Especially, this feature is useful for creating the molecular images in the CMYK color mode for publication.

Creating molecular images in CMYK for publication

While the images generated by CueMol (and POV-Ray rendering) are in the RGB color space in default, some scientific journals request images in the CMYK color space for publication. In such cases, if you create the molecular images in RGB and then convert them to the CMYK color space, you may experience unexpected change of images. Especially, the depth and three-dimensional effects are lost in the vivid colors.

cmyk-sample-rgb1.png ----> cmyk-sample-cmyk1.png

This problem particularly occurs when you are using colors that cannot be represented in the CMYK color space (e.g., green, cyan, and magenta in the above figure). So, if you are preparing your manuscript for such journals, you can avoid such unexpected changes of the colors in the images by using colors compatible with the CMYK color space. The color management feature of CueMol supports such selection of colors for the molecular graphics production in the CMYK color space.

Simple setup for CMYK color mode

By executing the menu "Scene --> Use color proofing" in the main menu, the color proofing mode is turned on for the active scene.


In the default setting, all colors used in the scene is converted to the CMYK color space, and then displayed in the main MolView. Namely, the colors representable in the CMYK color space are displayed as is, while those not representable (i.e., out of the color gamut, more precisely) in the CMYK are displayed after conversion to similar colors representable in CMYK. Strictly, the color profile Fogra27L CMYK Coated Press for the CMYK press printing is used in default.

cmyk-molview-rgb1.png cmyk-molview-cmyk1.png

(Left: color proofing turned off / Right: turned on with Fogra27L CMYK Coated Press profile)

Color proofing mode is turned off by executing the "Scene --> Use color proofing" in the main menu again, and all colors are displayed as is.

Color widget

In the color proofing mode, the color after the conversion in the CMYK color space is displayed with the warning mark in the color setting widget, if the specified color is "out-of-gamut" (i.e., out of the CMYK color space).


If no mark is shown, this means that the specified color is "in-gamut" (i.e., in the CMYK color space) and so the color will not change after the conversion to the CMYK mode. In contrast, if the warning mark is shown, the specified color is "out-of-gamut" and the color will change after the conversion to the CMYK mode.

Furthermore, you can convert the specified color to the in-gamut color (shown next to the warning mark), by clicking the warning mark.

cmyk-colwidget1.png --> cmyk-colwidget2.png

In the above example, the magenta color (#ff00ff) is out of the CMYK color space and so shown with the warning mark. By clicking the warning mark, the color is converted to the similar color in the CMYK color space (#bc6aa6), and then the warning is cleared. After clearing the warning, the color compatible with the CMYK color space is now stored, and thus the color will not change by turning on/off the proofing mode.

If you are creating the molecular graphics for the journal that requests the CMYK image format, it is better to check the all used colors are "in-gamut" by using this proofing mode (and the color warnings).


In the color proofing mode, the rendering of the images (e.g, POV-Ray rendering) is performed, after all of the colors used in the scene converted to the color representable in the CMYK color space. Although the output image is in the PNG format represented in the RGB color space, it will not change largely after conversion to the CMYK mode

lys-povray-rgb1.png ----> lys-povray-fogra27l-cmyk1.png

The above example shows the images created by the POV-Ray rendering (with color proofing mode turned ON), before (left) and after (right) changing to the CMYK mode.

Further details

Further detailed settings about the color proofing can be performed in the Scene's property page. There are three properties for color proofing in the Scene, as follows.

Specify the file name of ICC profile. The file is located in the "icc profiles" directory (see below).
Specify the rendering intent, i.e., the method to convert out-of-gamut colors to in-gamut ones. See for more detailed explanations about conversion.
If this value is true, colors are converted using the ICC profile/intent specified above properties.

The default directory for the ICC profile files is

 <CueMol installation directory>/data/icc_profiles

Namely, in the case of Windows, if you installed CueMol to the default location (i.e., C:\Program Files (x86)\CueMol 2.0), the ICC profile directory is "C:\Program Files (x86)\CueMol 2.0\data\icc_profiles".

If you want to use other ICC profiles than default, copy the profile file to this directory and set the file name as the property. For example, if you want to use Japan Color 2001 Coated, download the Adobe's ICC profile files, and copy the JapanColor2001Coated.icc file to the above directory, and then specify the file name (i.e., JapanColor2001Coated.icc) as the icc_filename property. If the profile is loaded successfully, the message like below will appear in the log window:

 Scene> Load ICC profile [C:\Program Files (x86)\CueMol 2.0/data/icc_profiles\JapanColor2001Coated.icc]: OK
 Scene> ICC profile info:
 Japan Color 2001 Coated
 Copyright 2002 Adobe Systems, Inc.

Last-modified: Thu, 23 Jun 2016 16:15:38 JST (1943d)