I am trying to get to Krokhotep in the Emperor's retreat but can't figure out the obelisk code?
You don't have to "figure out the obelisk code". After you defeated the Ice Giant, he gave you the code to open Krokhotep's door. I posted this reply yesterday to a similar question in this section:
"Sometimes it helps to "read the dialogue" again for your quest. When you open your quest log file, in each box for the quest, there is "question mark" in the upper right corner of the box. Click on it and you can see what you were told to do for that quest.
For this quest, Shalek told you that "after you defeated the Ice Giant, he showed you the combination to open the door to Krokhotep." Go back to the door for Krokhotep, and you will see several obelisks there. Light up just the obelisks that were in the combination. You said they were "alligator, snake, and tree". After you light them, the door should open."