On 03/05/11 14:08, Nalam, Madhavi wrote:
Hello all:
I am trying to generate a cif file for a new ligand using PRODRG server. The
server generates cif file without any problem. The problem comes when I try to
load the cif file in Coot and try to model the ligand into the electron density.
It gives an error message like this..
------------------------------------------------------
Failed to match (to the dictionary) the following model atom names:
XXX
"Cl38" "Cl39"
That would cause exploding atoms, so the refinement didn't start
-------------------------------------------
This problem never occurred to me before whenever I generate new cif files. The
ligand has two chlorine atoms. I tried to give different three letter codes for
the ligand assuming the three letter code I gave may already be in the
dictionary and that is why it is giving me the error message. I get the same
message irrespective of changing the three letter code.
I also tried generating a cif file by running it through Refmac5 (the job fails
and gives me a cif file which I used in Coot) and again I ended up with the
same message.
Check that the dictionary names and the atom elements for the Cl atoms
are upper-cased in both the PDB file and the dictionary.
Paul.
