Hal_Al and Carl have explained above how to account for the 1099-Misc by first putting the income in as reported on the form for computer matching, then go to "Other reportable income" and put in a negative number to subtract that income out and put in the description somehow saying reported in capital gains sec 1235.
Once you have accounted for the 1099-Misc and then subtracted it, then go to "Stocks, Bonds..." area and enter a long-term sale of "other" and describe as "1235 Patent sale" to get the income on schedule D.
Had you not gotten a 1099 then you could have just skipped to inputting a long term sale.
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