Thanks Kevin I'll check it out..
Curious what's the O+1 (in the atom field) that coot is adding on new nucleotides? sfall crashes out because it doesn't know how to calculate the scattering factor for this atom. F On Oct 25, 2011, at 9:44 AM, Kevin Keating wrote: > I just committed a fix for this to the repository. You can give it a try > once r3714 makes it to the compiled builds. The fix itself is from Huw > Jenkins, who also figured out a work-around: The problem only occurs when the > 3' nucleotide is a C, so just mutate the 3' terminal nucleotide to anything > other than a C, add a terminal nucleotide, and then mutate it back to a C. > > - Kevin > > On 10/24/2011 11:09 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
