Hi Scott, Congratulations for being up to date with you pre-release version.
AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad, Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear to me what your custom cif files contain. Coot renames residue name to match the dictionary. I'd be very surprised indeed if Coot changed the atom names (as you said it did). The Right Way, it seems to me, to fix this, is to "on-the-fly" change the dictionary identifiers to the PDB standard (this is what I believe Phenix does). This update is tentatively scheduled for 0.8. For the moment though, for handling cif/dictionary/atom-naming convention problems with Coot, I recommend the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. ________________________________________ From: Scott Classen [[email protected]] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: [email protected] Subject: mon_lib_list.cif? Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in.
