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
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