Is there finally, at long last, one convention for nucleic acids? I wonder how many cumulative person-years of exasperation this @#$% issue has caused?
And please note, even Mother Nature herself, let alone synthetic chemists, occassionally attaches U to deoxyribose or T to plain ribose. ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp ---- Original message ---- >Date: Mon, 12 Sep 2011 12:23:17 -0600 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of Francis E >Reyes <francis.re...@colorado.edu>) >Subject: Re: [ccp4bb] refmac and DNA (and now RNA) >To: CCP4BB@JISCMAIL.AC.UK > >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
