Dear Appu,

The map of the omitted region is indeed supposed to be just a box. It is provided so that you can verify that the region that was omitted is the region you wanted omitted.

If you want a nice picture of the remainder of the molecule, then I'd just calculate a 2mFo-DFc map after deleting the ligand. (As an aside, you could of course have calculated your SA-omit map that way too, just deleting the ligand and running SA refinement).

I hope that helps!
All the best,
Tom T

From: [email protected] [[email protected]] on behalf of Appu kumar [[email protected]]
Sent: Sunday, December 09, 2012 9:17 PM
To: [email protected]
Subject: [phenixbb] Simulated annealing map

Thank you Terwilliger, Thomas for you quick reply, for guiding me on how to make simulated annealing omit map. Now i am able to make it but i have one question. i want to show the SA omit map of ligand with the map of omitted region around ligand. I tried it, i got the map also, but the omitted map of region around ligand is show in recatangular box which is not as great as of ligand inside the omitted region.
Thank you