Ok I understand why it doesn't work.
But by default the mutation is in RNA? How to set it up for DNA.
The one I want to mutate is named Ad (and not Ar) and I want to mutate
it in Td and coot keep going to give me the error message about Tr...
Here is an overview of my pdb:
ATOM 22 P Ad I 7 -16.088 73.901 56.951 1.00
20.39 E P
ATOM 23 O1P Ad I 7 -17.394 73.886 57.646 1.00
21.78 E O
ATOM 24 O2P Ad I 7 -15.088 74.958 57.268 1.00
23.78 E O
ATOM 25 O5* Ad I 7 -15.403 72.460 57.129 1.00
22.09 E O
ATOM 26 C5* Ad I 7 -16.143 71.256 56.879 1.00
24.65 E C
ATOM 27 C4* Ad I 7 -15.542 70.063 57.592 1.00
24.16 E C
ATOM 28 O4* Ad I 7 -14.324 69.618 56.921 1.00
24.19 E O
ATOM 29 C1* Ad I 7 -13.192 69.825 57.743 1.00
24.39 E C
ATOM 30 N9 Ad I 7 -12.120 70.395 56.920 1.00
24.29 E N
ATOM 31 C4 Ad I 7 -10.970 69.745 56.524 1.00
23.22 E C
ATOM 32 N3 Ad I 7 -10.602 68.484 56.816 1.00
24.50 E N
ATOM 33 C2 Ad I 7 -9.420 68.194 56.258 1.00
22.46 E C
ATOM 34 N1 Ad I 7 -8.633 68.964 55.499 1.00
21.68 E N
ATOM 35 C6 Ad I 7 -9.037 70.224 55.221 1.00
22.11 E C
ATOM 36 N6 Ad I 7 -8.263 70.989 54.456 1.00
24.06 E N
ATOM 37 C5 Ad I 7 -10.266 70.655 55.753 1.00
23.56 E C
ATOM 38 N7 Ad I 7 -10.955 71.857 55.659 1.00
23.42 E N
ATOM 39 C8 Ad I 7 -12.043 71.653 56.365 1.00
24.40 E C
ATOM 40 C2* Ad I 7 -13.615 70.614 58.982 1.00
23.31 E C
ATOM 41 C3* Ad I 7 -15.132 70.406 59.015 1.00
24.25 E C
ATOM 42 O3* Ad I 7 -15.763 69.585 60.007 1.00
26.40 E O
by the way DNA is much cooler than RNA.
Pierre
On Apr 7, 2009, at 2:37 PM, William G. Scott wrote:
Looks like you might be mutating into RNA (hence the non-canonical
little r). But that is ok. RNA is inherently more interesting.
On Apr 7, 2009, at 10:48 AM, Pierre Aller wrote:
Hi all,
I am using the last version of coot on mac OS X. I tried to mutate
some nucleic acids and I encounter some problems.
It works fine for everything except for a mutation toward a Thymine.
I got this error message:
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 Tr
Is it a bug, or am I doing something wrong?
Thanks,
Pierre
Pierre Aller Ph.D.
Postdoctorate Associate
University of Vermont
201 Stafford Hall
95 Carrigan drive
Burlington, VT 05405-0084
Phone: 802-656-9534
mailto:pierre.al...@uvm.edu
