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]> 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]>: > > > 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]>: > > > >> 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]>: > >> > >>> 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] > >>> 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] > >> phone : +49 0931 31 84031 > >> ------------------------------------------------- > >> > >> ######################################################################## > >> > >> To unsubscribe from the COOT list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > >> > >> This message was issued to members of www.jiscmail.ac.uk/COOT, a > >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > > > > > -------------------------------------------------- > > Dr. Clemens Grimm > > Institut für Biochemie > > Biozentrum der Universität Würzburg > > Am Hubland > > D-97074 Würzburg > > Germany > > e-mail: [email protected] > > phone : +49 0931 31 84031 > > ------------------------------------------------- > > > > ######################################################################## > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/COOT, a > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > -------------------------------------------------- > Dr. Clemens Grimm > Institut für Biochemie > Biozentrum der Universität Würzburg > Am Hubland > D-97074 Würzburg > Germany > e-mail: [email protected] > phone : +49 0931 31 84031 > ------------------------------------------------- > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
