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
