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:[log in to unmask]
>>
>>