Dear Christian, Sometime ago, I ran into the same problems as you describe. I think I used an iUCR program to do the conversion. However, extensive manual editing was still necessary. The problem was that the cif file had long atoms names (5 characters), which got truncated upon conversion, resulting in different atoms having the same name. This probably explains the behavior you observe with coot.
I am not aware of a program which automatically invents new, unique atom names after truncation, so I am afraid you will have to do it using your favorite editor. You should also check the position of the atom name, so e.g. a C-alpha (CA) atom does not get interpreted as a calcium. Best regards, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Christian Roth Sent: Wednesday, August 17, 2011 10:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] conversion of ccdc cif to pdb Dear all, I want convert a small molecule cif into pdb. Unfortunately coordvonv failed with the following error message: CCP4I TERMINATION STATUS 0 "At line 537 of file /usr/local/xtal/ccp4-6.1.3/src/coordconv.f Fortran runtime error: Bad value during floating point read I am able to read the file with pymol and see the structure, unfortunatley one cannot isolate chains or atoms. Some atoms exists twice and if one delete it in Coot one delete always more than one atom and that is not what I want. Does anyone know a good programm to deal with cif file or to convert it properly in a format? Thanks in advance Christian
