Yes, new version of the dictionary uses U. Refmac will read right or left justified residue names, however pdb may use only one of them.
There are some backward compatibility code/dictionary elements. For example Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3 residue/atom names. It will make sure that all software use same naming convention and moving between them is smooth. Hopefully we all will have one naming conventions. regards Garib On 12 Sep 2011, at 19:23, Francis E Reyes wrote: > Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for > RNA residues in the residue field. > > This is with a recent refinement with refmac 5.6.0117 . > > And of course this switch in naming convention breaks compatibility with > molprobity (which requires right justified letters in the residue field) > > > F > > > On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote: > >> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I >> have found a problem working with DNA that I have not seen with >> 6.1.13/5.5.0109. Namely, >> >> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to >> output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac >> fails with the warning that it found a new monomer. It appears that it >> stumbles upon the very first thymidine, but in a strange twist it >> reports the problematic residue having the name "DY"! >> >> - if I use the pdb file previously produced by refmac, which has the >> A/T/G/C as residue names, it fails too but now complains about the "new" >> monomer named "T". >> >> - the workaround I found is to rename all the thymidines to "DT". It is >> a bit annoying since coot keeps renaming them (well, not refmac/ccp4 >> problem per se) and I have to rename back (easily scripted task, of >> course). What is peculiar is that Ad/Gd/Cd don't need to be renamed >> (does this have anything to do with thymidine being the only one that >> changes residue name in RNA?). >> >> Has anyone else seen this or it's something specific to my setup? >> >> Cheers, >> >> Ed. >> >> -- >> After much deep and profound brain things inside my head, >> I have decided to thank you for bringing peace to our home. >> Julian, King of Lemurs > > > > --------------------------------------------- > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
