Dear Urmi, This has been the subject of long-threads in the past and belongs to the same category as the yearly linux vs. Mac discussions. By searching the archives, you should be able to get all the information you want, and even more!
Here is my (personally biased) summary: Lowering the occupancies to get reasonable B-factors is about the worst you can do: In this case even medium expert users may now think that the side chains are well defined since they have reasonable B-factors, while in fact, they are not well-defined at all. The two main camps are as follows: A) leave the extremely high B-factors as they are. In my view this is the best description of the truth: The side chains are there, but we cannot see them because they are too floppy, as evidenced by the very high > 100 B-factors. B) Set the floppy side chains to absent because we have no experimental evidence about their position. This is usually done be either removing the side chain atoms altogether, or by setting the occupancies to zero. I won't go into the pros and cons of each approach, this has been discussed ad nauseam in the past. Again, if you are interested, search the archives. My 2 cts, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Urmi Dhagat Sent: Thursday, February 21, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I have a question about B-factors and occupancies of side chains - I am working on a 2.8 A structure which is missing density for some of the side chains (especially the floppy ones like Lysine/Argenine, Glutamine) in loop regions and the B-factors for these side chains are over 100. I was wondering if it is ok to drop the occupancies of these residues or side chains to lower their B-factors? Or do I leave them as is? Urmi Dhagat
