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
