I may not be doing it right, but I cannot get mutate_nucleotide_range to
work. To test, I create an ideal DNA with AAAA sequence. Mutating it
from GUI does not work - thinks it's a protein. But I actually do want
to use it from python script, so according to the manual
mutate_nucleotide_range is the way to go. So I try to use this as a test
mutate_nucleotide_range(0, "A", 1, 4, "ATGC")
which kind of works except that it refuses to mutate to thymine, saying this
>This should never happen - badness in get_standard_residue_instance,
we selected 0 residues looking for residues of type :Tr:
>Oops - can't find standard residue for type T
>(mutate-base 0 "A" 2 "" "T")
Notice Tr - despite the fact that I am mutating DNA, not RNA.
Furthermore, residue types indeed change to RNA (e.g. DA->A) in the
output file, and mutating to AUGC works fine.
Interestingly, point mutations to Thymine work just fine. I poked
around the source code, but so far cannot track down where it wrongly
decides it to be an RNA.
I can probably get what I need to work by deleting nucleotide side
chains, renaming residues outside of coot and then using fill partial
residues tool. I did not try whether this will work yet, but is
mutate_nucleotide_range buggy or do I have to somehow specify polymer
type before applying it?
This is on revision 4549.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
