Dear Madhavi,
How did you generate the cif file? Did you make sure that CL1 and CL2 are
defined as atom.type_symbol CL and not C? If you used e.g. prodrg with your old
file with old positions of the CL atoms, prodrg will have generated a cif file
with atom types C instead of CL.
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nalam,
Madhavi
Sent: Wednesday, May 11, 2011 4:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] still having problems with Chlorine atoms in ligand during
refinement
Dear All:
Thanks to all who responded to my email. As per suggestions, I changed the
position of CL atom in the PDB file as below.
Before the Refmac refinement, the file looks like this...
HETATM 1662 O27 MK5 C 200 23.772 24.629 11.196 1.00 20.00 O
HETATM 1663 O1 MK5 C 200 14.877 35.704 18.421 1.00 20.00 O
HETATM 1664 CL1 MK5 C 200 21.096 24.148 10.673 1.00 20.00 CL
HETATM 1665 CL2 MK5 C 200 21.314 24.896 8.267 1.00 20.00 CL
After Refmac refinement, it looks like this, essentially CL is changed to
carbon atom. What should I do to make Refmac recognize as Chlorine atom?
---
ATOM 3126 CL1 MK5 C 200 20.830 24.051 10.574 1.00 29.27 C
ATOM 3130 C28 MK5 C 200 21.972 24.331 9.610 1.00 33.36 C
ATOM 3132 CL2 MK5 C 200 21.488 25.026 8.303 1.00 30.57 C
ATOM 3136 C26 MK5 C 200 23.074 25.080 10.390 1.00 32.43 C
I have chlorine atom as CL in both the PDB file as well as in cif file.
Any inputs will be greatly appreciated,
Thanks and have a nice day,
Madhavi
From: herman.schreu...@sanofi-aventis.com [herman.schreu...@sanofi-aventis.com]
Sent: Wednesday, May 11, 2011 3:55 AM
To: Nalam, Madhavi; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Chlorine atoms in ligand during refinement
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nalam,
Madhavi
Sent: Tuesday, May 10, 2011 9:18 PM
To: CCP4BB@JISCMAIL.AC.UK
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
