And in fact it doesnt..
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
MDO MDO
"{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid" *NON-POLYMER * 24 14 .
#
On Thu, 21 Sept 2023 at 21:53, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:
> Check the dictionary has labelled it as peptide
> like ALA
> data_comp_list
> loop_
> _chem_comp.id
> _chem_comp.three_letter_code
> _chem_comp.name
> _chem_comp.group
> _chem_comp.number_atoms_all
> _chem_comp.number_atoms_nh
> _chem_comp.desc_level
> ALA ALA ALANINE *peptide* 13 6 .
>
> On Thu, 21 Sept 2023 at 18:58, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
> wrote:
>
>> On 21/09/2023 18:05, Kelvin Lau wrote:
>> > Dear all
>> >
>> > I am having trouble with an unnatural ligand/amino acid.
>> >
>> > I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO
>> residue that replaces three residues in a series G-A-S-G-D to become
>> G-MDO-D. MDO is in the Coot library.
>> >
>> > I have been very used to replacing cysteines with CME with
>> Modelling>Replace residue. It works great, removes the OXT and all the
>> other atoms, can use real space refine directly.
>> >
>> > For this MDO residue I find that it correctly fetches from the
>> dictionary, however, I cannot refine it. Whenever I click on an atom and
>> drag it just blows up or the atom gets stuck.
>> >
>> > I have now opened up 6Q6H and 7TQR and tried to just refine the built
>> in MDO in those PDB, same thing happens.
>> >
>> > Does anyone have any ideas of what might be going on? Also in general
>> for modified residues/unnaturals.
>>
>>
>> If you tell Coot that the group is a non-polymer it will believe you.
>>
>> Use the Restraints editor to change the group to "peptide" (not tested).
>>
>> Paul.
>>
>> ########################################################################
>>
>> 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/
