Check the PDB - looks like you defined them as C rather than Cl somehow. Check their temperature factors, I bet they're way lower than the rest of the ligand.
Also the arginine residue in the top left corner seems to be mis-modeled - there's a water molecule where its end should be (and a nice negaive density peak near the wrong position). Artem On Tue, May 10, 2011 at 2:18 PM, Nalam, Madhavi <[email protected]>wrote: > 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 >
