Hi all, My work flow is between coot and phenix.refine using only PDB version 3 DNA atom/res names.
Currently my temporary work around is to do a global substitution using vi. Assuming your DNA is chain D then the following 2 lines entered at the command line will update the dna_from_coot.pdb file to version 3 happiness. vim -c "argdo %s/ Gd D/ DG D/ge | %s/ Td D/ DT D/ge | %s/ Ad D/ DA D/ge | %s/ Cd D/ DC D/g | %s/O1P/OP1/ge | %s/O2P/OP2/ge | %s/C5M/C7 /ge | update" dna_from_coot.pdb vim -c "argdo %s/ O5\*/ O5'/ge | %s/ C5\*/ C5'/ge | %s/ C4\*/ C4'/ge | %s/ O4\*/ O4'/ge | %s/ C1\*/ C1'/ge | %s/ C2\*/ C2'/ge | %s/ C3\*/ C3'/ge | %s/ O3\*/ O3'/ge | update" dna_from_coot.pdb Scott On May 26, 2010, at 2:46 AM, Paul Emsley wrote: > 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.
