On 08/09/11 15:35, 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"!
Weird. I'm using Coot 0.7-pre1.3628 ( a bit ahead of yours but not so much? or maybe yes? ) and DNA residues are saved in what I think it is PDB v3 format ( DA, DC, DG, DT ) These files are properly understood by refmac 5.6.0119, which at the end produces coordinate files in the same format ( so DNA residues are: DA, DC, DG, DT ) The only heck with coot/thymidines is that if you "add a terminal" T or mutate another DNA residue to T, it lacks its C7 ( formerly C5M ) atom. However, if you build an ideal T, it has C7... My workaround is to add those pesky C7 atoms in dummy positions and refine. > > - 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". Not what I find (see above) > > - 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? > Perhaps the Nd/DN issue was solved between revisions 3470 and 3628 ? Best, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
