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
