Hello:
There are two chlorine atoms in the ligand that I modeled in the active site. When I first modeled the ligand, the density is very clear for the ligand. The chlorine atoms were seen as white (different color than carbon atoms). After one round of refinement, there seems to be positive density around the two chlorine atoms (please see the attached file) while the density around the rest of the ligand seem to be very clear. I tried to model two conformations thinking that there is some disorder but still the positive density doesn't disappear. After a closer look where I just modeled one conformation for the ligand, the 2Fo-Fc density seem to be clear for the entire ligand and the positive density that appeared could be a problem with scattering factor. One reason for me to think this way is now the chlorine atoms are of the same color as carbon atoms.
I use version ccp4-6.1.13/Refmac5.5.0109 respectively.
Can anyone suggest what is going on?
Thanks in advance,
Madhavi
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