Dear Norman, Refmac version 5.0 sounds unlikely, the version with CCP4 6.3 is 5.7.0029. Anyway, your DNA seems to have asterisks in the atom names, which is 'so last decade' (they were removed in 2008). Refmac and Coot may not be equally forgiving for legacy formats. IMO neither should be. The best you can do is upgrade your PDB to a new format. There is a tool in CCP4i for that and the MolProbity server can do it as well.
HTH, Robbie Date: Sun, 26 Aug 2012 00:40:02 -0700 From: [email protected] Subject: [ccp4bb] compatibility issue between coot and refmac To: [email protected] dear ccp4 forum Does anybody know which version of coot is compatible with which version of ccp4i, or more specifically, refmac? I seem to be having DNA recognition problem between the two softwares. I haven isolated the problem to the differences between naming conventions. However, manipulating the naming convention would only cause the pdb file to work in one of the software but not both. If it works for refmac the real space refinement in coot would not work. The warning sign pops up for that would says 'failed to match these atoms names (O1P, C5*...etc)to the dictionary' and if it works for the coot the refmac would not process the pdb file at all. Naturally the first thing i thought of to do is to synchronize the dictionaries in both of these programs but doesn't seem to be that straight forward. I suspect it has something to do with the import cif dictionary but i don't know where to import it from. That's why i think it might be easier find a version of coot that's compatible or vice versa. The versions of programs i currently running on are coot 0.6.2 and ccp4 6.3.0 interface 2.2.0. The version of refmac in ccp4 is 5.0. Please let me know if I am on the right track or if there is a easier way to do this. Thanks Norm
