P.S. I would set the occupancy to zero for those parts which you don't see density but I would never remove them unless you know that your ligands has been degraded.
On Aug 23, 2011, at 2:36 PM, Francis E Reyes wrote:
Seems to be a quiet day on the BB, so I propose this question:
Suppose you have a ligand in the binding pocket and some mediocre data (3 A or so), the 'core' of the ligand is well defined in 2Fo-Fc map using the model phases of your protein, however there are 'chains/tails' of the ligand which are not. Composite omit or simulated annealing omit maps do not produce density for these 'chains'
The question here is how the chains/tails should be modeled (if at all).
[1] Model in the core, but remove the atoms for the chains (and conclude the diffraction data do not support interactions with the protein and subsequent experiments are needed (higher resolution data, biochemical data, etc)).
or
[2] Model in the chains/tails noting that potential hydrogen bond donors/acceptors on the protein are within hydrogen bonding distance to the chains/tails. You do this and subsequent refinement still does not produce the expected density for the chains.
or
[3] Your solution here.
If this situation has been discussed before, please let me know .
F
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder