I'm using Adobe Indesign to write my Chemistry PhD thesis. I'm far from an expert in publishing/design, so please forgive me if this is a simple question.

I am having an issue with an few images that I have placed in Indesign (they were generated from another program called Pymol, where Pymol created the .png in CMYK. These placed images in Indesign seem to be changing the colours of other images on the same page. The usually vivid blue is now pale.

I am worried that when I publish my thesis to pdf it will have miss-matched blues. What should I do to "fix this". I cannot really remake the CMYK images in RGB, because they took me quite a while to make and annotate them.

  • Is this effect only visible in InDesign's on-screen preview, or also in the finished .pdf?
    – Vincent
    Commented Aug 20, 2018 at 10:11
  • 2
    PNGs are RGB (and sometimes Indexed colour). The format doesn't support CMYK. Perhaps you have this backwards? If you want an image format that supports CMYK, probably best to use TIFF.
    – Billy Kerr
    Commented Aug 20, 2018 at 11:29

1 Answer 1


"Pymol created the .png in CMYK" - This is erroneous in one of two regards: PNG supports RGB, Indexed color and grayscale only, so if you are getting a CMYK image from Pymol, it isn't a PNG. Alternatively, if you are getting a real PNG, it isn't CMYK.

Fortunately, that doesn't really matter (that much). When you export your document to PDF, you can select a PDF/X standard (PDF/X-1a:2001 is a tried and true standard) from the "Standard" dropdown menu to convert the entire PDF document to CMYK (with spot swatch support) on output. PDF/X also forces fonts to embed, and does myriad other things to make the document conform to the given PDF/X ISO standard. All of this is intended to help the PDF to print more consistently and reliably. Just be aware that active content like form fields and comments are not allowed in this standard.

  • PNGs also support Indexed colour, but you are right, the OP doesn't have a CMYK PNG because there is no such thing.
    – Billy Kerr
    Commented Aug 20, 2018 at 13:20
  • I was under the impression that indexed color was a subset of RGB.
    – 13ruce
    Commented Aug 20, 2018 at 15:34
  • Or, rather, a method used to organize RGB color values. I suppose the inclusion of grayscale means I was simply incorrect. Thanks for the correction.
    – 13ruce
    Commented Aug 20, 2018 at 15:36

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