]I don’t want automatic capitalization of the word following spp. , or an abbreviation of a species name I use frequently.
In other words, I want to be able to write “E. coli” without having to go back and change the c in coli from upper case to lower case.
It would be nice to be able to do auto-fill, including italicization, for my commonly used scientific names, say Mycobacterium bovis. Remember that scientific names are always in italics.
Thanks!
Check out Scrivener->Preferences->Corrections. There are settings there to not capitalize sentences, which is what is happening when you enter a period. I don’t think it’s possible to make Scrivener use italics on any custom substitutions, since it’s trying to just match whatever font settings you are using at the cursor.
The rub is that I want Scrivener to capitalize the beginning of sentences, but not capitalize after a single upper case letter followed by a period.
My therapist informs me I want too much out of life and should lower my expectations, and this may be yet another case in point. 
You can just ignore the false capitalization, and set up a Substitution in your compile settings, so that it replaces the upper-case “Coli” with “coli” on the output. As long as none of your sentences start with Colic, Colicky, colic root, Colima, Colin Powel, Coliphage, Coliseum, Colitis, and so-forth… then you’ll be fine. 
That’s a good solution. It will be a bit tough, though, as a lot of my stories begin with “Colicky Colin Powell got Colitis at the Coliseum.” Nothing like a general in public with diarrheal disease to grab a reader’s interest.
Actually, have you tried adding a custom auto-correct for “e.” that replaces it with "E. coli "? I think in that circumstance, it might not auto-cap the c, especially if you add in a space at the end.
An auto-typing program might help with these matters.
I use Typinator and think it’s great.
Have a manuscript that uses repeatedly a place name in Tanzania:
Ngorongoro, Ngorongoro, Ngorongoro
The Masai say that’s the sound of the bells on their cattle.
Pronounced uhn gore ahn GOro
In Typinator, it’s three letters, NGR (in lower case)
Looks like that would do the italicising as well?
Can I use Typinator inside Scrivener?
Typinator (and programs like it) works inside any and every program that you use.
And yes, you may set up font/size changes as well, so that a term always appears in italics.
You may create sets of abbreviations that yield expansions, some of them quite long.
I have a bunch for all those bits of typing I have to enter over and over:
credit card numbers, e-mail addresses, zip code, urls, etc.
It’s possible to type 3 letters and generate the entire Gettysburg Address.
Typinator didn’t run well (at all) on my computer (10.6.8), and I had to use the kill command to get it to quit. Any better recommendations?
Sure: write to the people at Ergonis and ask what went wrong.
You may have a known conflict that they can help resolve.
Also, consider upgrading to 10.8.
Though I doubt that 10.6 is the problem.
Did you also try shutting down and rebooting after the failure?
And then run Disk Utility, to clean up permissions problems.
There’s a free utility called Onyx; I run it every month.
It cleans up the clutter that builds up in system files and caches.
Typinator is highly rated; I bought it because others on this forum vouched for it.
Thanks, I’ll give it a try. I am getting really tired of typing B. henselae and then fixing it a gazillion times.
Text Expander? Seems to be working well for me.
This annoyance applies to the use of any abbreviation, not just scientific ones. I find this so extremely frustrating that I’ve turned off the sentence capitalization feature altogether. The PITA of fixing Scrivener’s brain-dead auto-corrects completely outweighs the inconvenience of making my copyeditor scan for capitals at the beginning of sentences.
The addition of a “don’t-change-what-I-have-typed” whitelist would be welcome. I could put all my abbreviations like S. cerevisae, scientific terms with irregular orthography like pH, and such in the list once and still use the auto-cap feature.
NeoOffice has a capitalization exceptions list. As does OpenOffice and M$ Word (I think) so it is obviously something that can be done.
I’d recommend you take a look at TypeIt4Me.
ettoresoftware.com/products/typeit4me/
Can’t fault it in any way. 