Oops this occurs with svn 3633. I know this isn't the 'latest' but the 'latest' is having trouble compiling in SL for now... and it doesn't seem (from the svn logs) that much has changed with regard to this issue.
F On Oct 24, 2011, at 9:09 AM, Francis E Reyes wrote: > This seems to still be a problem for me. Adding a nucleotide to the 5' end it > works fine, but adding to the 3' end gives me the following error: > > > ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: -1 > mol_base_is_purine: -1 std_base_is_pyrimidine: 0 std_base_is_purine: 1 > mol_res_name: C std_base_name: A . > > > Thanks! > > F > > On Aug 16, 2011, at 2:21 PM, Kevin Keating wrote: > >> I think I've fixed the problem for adding RNA nucleotides. One of the >> internal Coot functions wasn't fully updated with the new residue names (i.e >> A and C instead of Ar and Cr). Try out 0.7-pre-1 revision 3628 when it gets >> packaged for OS X and let me know if it works. Paul, should I back-port the >> fix to the 0.6.2 branch? It's no extra effort, but I wasn't sure if you >> wanted to completely freeze that branch. >> >> Also, as long as the subject of RNA has come up, I wanted to throw in a >> shameless plug for RCrane (http://pylelab.org/software/#rcrane). It's a >> Coot plugin that partially automates the building of RNA in maps of up to ~4 >> A resolution. I just released a new version of it last week (version 0.7), >> and I'd love to hear any feedback on it. >> >> - Kevin >> >> >> On 8/16/2011 5:01 AM, Huw Jenkins wrote: >>> Hi, >>> >>> Yet another reply to one of my own posts! Some more information though. >>> >>> I've now hacked the coot.info in fink and compiled the latest pre-release >>> so I'm now running: >>> >>> 0.7-pre-1 (revision 3627) [with guile 1.8.8 embedded] [with python 2.7.2 >>> embedded] >>> >>> The library was still the old version so I replaced /sw64/share/coot/lib >>> with the directory from >>> coot-0.7-pre-1-revision-3627-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz >>> >>> If I build DNA using the ideal DNA/RNA builder I can add nucleotides on to >>> either end no problem. If I build RNA I get: >>> >>> ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: >>> 1 mol_base_is_purine: 0 std_base_is_pyrimidine: -1 std_base_is_purine: >>> -1 mol_res_name: U std_base_name: A >>> >>> Also if I mutate to Thymine using simple mutate C7 is missing (as reported >>> a few days ago). >>> >>> Hopefully that'll help finding out what the problem is... >>> >>> >>> Huw >>> -- >>> Dr Huw Jenkins >>> Astbury Centre for Structural Molecular Biology >>> University of Leeds
