Hi Ming,
One Uses "DT" in DNA. One doesn't use "T" in RNA, one uses
methyl-uridine, specifically 5MU. Poor old Coot gets confused if you try
to insert an RNA base into a DNA strand. And doubly so for thymine.
> I have a similar error on MacOS Coot 0.8.9.3 EL
That's an Old Coot. Maybe that's the problem.
Paul.
On 07/02/2021 15:53, Ming Sun wrote:
I have a similar error on MacOS Coot 0.8.9.3 EL, for DNA mutating.
Error: cannot find the standard residue for "Tr"
(1) using GUI "simple mutate" to mutate it to "T" on a DNA mol
(2) running python script "mutate_nucleotide_range(0,"C", 1, 2, "CT")"
I was also reading the other old posts about mutating DNA bases.
However, it would work for "U" but not "T".
Is there another version that I should try? Any inputs are warmly welcomed
Thanks again!
Ming
On Fri, Dec 4, 2020 at 4:05 AM Clemens Grimm
<[email protected]
<mailto:[email protected]>> wrote:
A test with Coot 0.8.9.2 EL gives back this Error:
(mutate-base 0 "T" 3 "" "A")
(is-nucleotide-chain-p 0 "T")
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
Zitat von Clemens Grimm <[email protected]
<mailto:[email protected]>>:
> OK, I did some quick tests and can confirm that Coot reliably gives
> back "0" for Ts. I guess that this related to a DNA(T) bug (see my
> previous posts).
>
> Is there a Coot version that does the job correctly?
>
>
>
>
> Zitat von Clemens Grimm
<[email protected]
<mailto:[email protected]>>:
>
>> Dear All,
>>
>> I am doing:
>> coot> (mutate-residue-range 8 "N" 5 60
>> "AGCTTAAAAATTGAAAAACTATTTTTTTTTTTTTTAAATCCATAACCCACTTGGGG")
>>
>> which gives me back:
>> (1 1 1 0 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 0 0 1 1 1 1)
>>
>> As the result does not look as expected I am unsure
>>
>> - whether a 0 in the result means error/nothing done/nothing to
do ?
>> - whether "AGCTTA ..." has to be written as "dAdGdCdTdTdA ..."?
>>
>> Regards,
>> Clemens
>>
>>
>>
>>
>>
>>
>>
>> Zitat von Clemens Grimm
<[email protected]
<mailto:[email protected]>>:
>>
>>> Dear All,
>>>
>>> mutating RNA bases to Tr gives me the following error:
>>>
>>>
>>> "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"
>>>
>>> Other residue types work well.
>>>
>>> There is a very old thread stating this (or a similar) error had
>>> been fixed for DNA. Maybe it had not for RNA?
>>>
>>>
>>> Clemens
>>>
>>> --------------------------------------------------
>>> Dr. Clemens Grimm
>>> Institut für Biochemie
>>> Biozentrum der Universität Würzburg
>>> Am Hubland
>>> D-97074 Würzburg
>>> Germany
>>> e-mail: [email protected]
<mailto:[email protected]>
>>> phone : +49 0931 31 84031
>>> -------------------------------------------------
>>
>>
>>
>> --------------------------------------------------
>> Dr. Clemens Grimm
>> Institut für Biochemie
>> Biozentrum der Universität Würzburg
>> Am Hubland
>> D-97074 Würzburg
>> Germany
>> e-mail: [email protected]
<mailto:[email protected]>
>> phone : +49 0931 31 84031
>> -------------------------------------------------
>>
>>
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> --------------------------------------------------
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: [email protected]
<mailto:[email protected]>
> phone : +49 0931 31 84031
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Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: [email protected]
<mailto:[email protected]>
phone : +49 0931 31 84031
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