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) = Unknown DNA ("Y" from "deoxY...", since UND is already taken by
undecane)
UNR (or UKR) = Unknown RNA
While their meanings may not be as immediately apparent as that of UNK, all of
these are currently unassigned, at least according to Coot's "Search Monomer
Library..." dialog.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jul 7, 2015, at 8:13 AM, Bernhard Lohkamp
<[email protected]<mailto:[email protected]>> wrote:
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/). Then you can use UNK in "mutate" functions. I (*) am
reluctant to add it to the amino acids for all since the PDB (nowadays) says
(http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp.three_letter_code.html):
For ambiguous polymer components three-letter code should be given as 'UNK'.
So UNK is not only for (unknown) amino acids any more...
B
(*) Not sure what Paul thinks
On 27/06/2015 19:02, Ethan Merritt wrote:
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
unknown identity.
I would also suggest being able to set this as the default type for new
residues - it allows easy recognition of amino acids that are as yet
unassigned, and avoids confusion with alanine.
I like that idea a lot.
Ethan
Cheers,
Oliver.
--
***************************************************
Dr. Bernhard Lohkamp
Associate Professor/Docent
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: [email protected]<mailto:[email protected]>
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