Dear Madhavi, Here are my comments: 1) as Artem mentioned, the arginine is clearly misfitted. 2) from the shape of the difference density, I have the impression that the terminal of your ligand is misfitted as well, eg. The central carbon atom between the two chlorines in the front instead of in the back and that you have to rotate the terminal by 180°. However, since the picture is mono, it is just a guess. 3) It may be that your chlorine converted to a carbon. Open your pdb file with an editor and check that the atom name of the chlorine is one position to the left with respect to carbons (see example below). Also check that the atom type on the far right is CL and not C. Also check your .cif files etc. that you have chlorine and not carbon. Some programs like to generate Cl (l small cap) instead of CL, which also causes troubles and Cl must be converted to CL. Good luck! Herman
HETATM 3356 C3 INH I 1 -35.181 11.563 23.045 1.00 40.99 C HETATM 3357 CL4 INH I 1 -34.143 11.710 24.418 1.00 41.43 CL -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Nalam, Madhavi Sent: Tuesday, May 10, 2011 9:18 PM To: [email protected] Subject: [ccp4bb] Chlorine atoms in ligand during refinement 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
