PDF creation with subscripts yields terrible results

I have a document with several chemical formulae and when I create a pdf, the quality is absolutely terrible.
Is there a fix for this, or am I doing something incorrectly?

I have to apply all the substitutions manually to create the non-fake subscripts?
The idea in the Unicode and TrueType project is that you keep your plain text plain. If you keep your plain text plain, content-based operations like searching, spell-cheching and sorting are not corrupted, no matter how complex the composition is. In other words, you insert a firewall between your character codes (the content) and your glyph codes (the appearance).
Now, this won't work if you do not have a graphical desktop display and a graphic deskside printer. In other words, it won't work in the world of the nineteen-eighties. Fortunately, this is not the world in which we are working. Separate processing of character codes and glyph codes was first discussed at the WWDC in May 1989, and first demonstrated it at WWDC 1992 with Apple Hoefler Text, by the way. It has been in the OS since System 7.5 in August 1994.
So, you use the GUI. You use Unicode / ISO-IEC 10646 as the space within which you code your text. And you use the simple glyph substitution of base TrueType and the smart glyph substitution and smart glyph shaping of advanced TrueType to get the appearance you want. Or in other words, you use Unicode to match the meaning and TrueType to match the mark.
With a document window open and the cursor in the column, you specify the style for simple glyph shaping by selecting any TrueType/OpenType font. Inside the font there is an obligatory table, the CMAP Character Map. This table defines the character codes that the font is able to image, and the default glyph codes with which those character codes are imaged in that specific font.
With your Typography Palette open, you can see if the font only has obligatory Character Map shaping to default appearances, in which case it says "No typographic features in this font," or there are substitutions for smart shaping and smart scaling. For instance, if you select Hoefler Text you will find that there are smart substitutions for superiors (superscripts) and inferiors (subscripts).
If you want to see the glyph codes and corresponding glyph drawings in an intelligent font file, then you open the Apple Character Palette, from the View menu you select Glyph, from the Font menu you select the family name e.g. Hoefler Text, and from the style menu you select the family member. Take the time to move your cursor over the glyph drawings.
In the co-ordinate system, e.g. click glyph code 801. You will see a popup that says GID 801, that is, glyph identifier 801. The glyph identifiers (glyph codes) are private to and specific to the font file. They are not cross-font. There is no corresponding character code! Is this a bug in the font? No, it is as designed, because you do not draw ligature long s, long s, and l as a character code.
The font only draws default glyph codes by depicting them directly onto character codes. If the type designer wants alternate stylistic appearances for the default glyph codes and their glyph drawings, she uses the smart substitution support. The smart substitution support takes the output of the obligatory CMAP Character Map transform, which is default glyph codes, and remaps that to alternate glyph codes for alternate glyph design appearances.
This means that the vast majority of glyph codes in a font file may be drawn by depiction onto other glyph codes and not onto character codes. For instance, try counting the number of glyph codes in Apple Hoefler Text or in Linotype Zapfino that are not directly depicted onto character codes. So, you can have perfect legibility at the level of appearance, and your character codes can be perfectly plant at the level of content. This has been possible since System 7.5 in 1994.
What you cannot have today is searchable softcopy. Because the meaning of the glyph designs is in the indices of the intelligent font, and those indices are not supported at all in PostScript, and are not supported in PDF until versions higher than 1.3 which is the PDF version supported by OS X. These problems have existed for many, many years. PostScript does not support the intelligent separation model of the International Color Consortium, just as it does not support the intelligent composition model of the Unicode Consortium.
/hh

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