Dear Jared
There are existing het groups in the PDB chemical component dictionary for
unknown amino acid
pdbe.org/chem/UNK
unknown RNA nucleotide
pdbe.org/chem/N
unknown DNA nucleotide
pdbe.org/chem/DN
unknown RNA purine base
pdbe.org/chem/P5P
unknown RNA pyrimidine base
pdbe.org/chem/Y5P
R
So UNK is not only for (unknown) amino acids any more...
This has me wondering, would it be possible (or useful) to specify unknown
amino and nucleic acids with an extension of the UNK (and UNX, UNL)
three-letter codes?
Perhaps something like:
UNA (or UKA) = Unknown Amino acid
UNY (or UKD) = U
For new amino acids you can use:
set_add_terminal_residue_default_residue_type("UNK")
Then you get an UNK (no CB) instead of ALA.
As for mutation, you have to go via ALA and then rename it.
Alternatively you can append UNK to your standard-residues.pdb (found in
$COOT_PREFIX/share/coot/). The
In case it is useful to anyone else, this function seems to work fine:
def mutate_residue_range_by_click_a():
def mutate_residue_range_by_click_b(res1,res2):
if (res1[1]!=res2[1]) or (res1[2]!=res2[2]) or (res1[3]==res2[3]):
info_dialog("Start and end points must be in the same mol and
On Saturday, 27 June 2015 04:39:56 PM Clarke, Oliver wrote:
> I would still ultimately favor making it a standard residue with three letter
> code UNK and single letter code X - it allows for easy specification of
> ambiguity, and it is the PDB-sanctioned way of representing an amino acid of
>
That should work for the moment, thanks Bernhard! I can’t use it with
mutate_residue_range because there is no single letter code, but I can loop
through all residues in a range sequentially and mutate to ala and then set the
residue name, so that works fine.
I would still ultimately favor mak
How about using:
set_residue_name(int imol, const char *chain_id, int res_no, const char
*ins_code, const char *new_residue_name)
B
On 26/06/2015 18:36, Oliver Clarke wrote:
Hi all,
Would it be possible to add "UNK" to the list of standard residues one can mutate to?
Currently mutate doesn
Hi all,
Would it be possible to add "UNK" to the list of standard residues one can
mutate to? Currently mutate doesn't seem to work using "UNK" as the target res
type, and I would like to add it to a function for mutating a residue range to
poly-UNK.
This is useful where one has a structure c
