When building an RNA sequence containing GU, the phosphorus on
the U and the two non-bridging phosphate oxygens get coordinates
0.000 0.000 0.000
Oddly, this only happens on the strand specified by the user. The
complementary strand does not have this problem.
In other words, if I build double-stranded A form RNA and input
the sequence
GUAC
and look at the duplex pdb file, the problem only arises on one
strand (the a strand). The b strand, which is symmetry-identical,
is fine. Also, if I make an RNA sequence but use GTAC, it works
ok.
My workaround has been to chop out those coordinates and
regenerate them in CNS. The bond distances between the P and
the bridging oxygens, however, wind up being a bit too long until I
minimize the model.
Also, the pdb files generated aren't canonical.
This fixes it: http://tinyurl.com/2zrh2
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