Bob
I assume that there is more than just one stock sold and purchased during the year so just to give more detail. Most likely the brokerage account also has a cash component as well as the investments. So in addition to the S Corp operating Checking, I would set up the brokerage checking and then the brokerage investment accounts.
You buy 100 share of Microsoft at $60
Debit Investment Account $6,000
Credit Brokerage Cash $6,000
When you sell the shares at $104 for your $4,400 gain the entry is
Debit Cash Brokerage $10,400
Credit Investment Account $6,000
Credit Income S/T Gain $4,400
Same result as Seaside above mentioned it is just that you will most likely need an Investment Asset account on the books tracking basis and the end of the year basis. If you are doing GAAP financials you probably need to adjust the stocks to FMV.