I think you'll find that this is not a naive question...... I doubt there is a consensus for this. Neither option is ideal, mainly because of possible confusion generated for non-crystallographers. My preference is to include the side chain but set the atoms i do not see to zero occupancy. The PDB does not like this however.... Others will probably chime in here; in any case i think this has been discussed before, so digging in the archives might help as well.
Bert ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Sasha Pausch [[email protected]] Sent: Tuesday, November 11, 2014 1:14 PM To: [email protected] Subject: [ccp4bb] Amino acid side chains without density Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?
