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
