[Chimera-users] Stuck in adding residue in the C-terminal of a segment

[Prathit Chatterjee]

Dear Dr. Meng,

Thank you for your suggestion. I took the second suggestion and it worked.
The first one was seeming a bit non-trivial because the PRO already had a
C=O group in the C-terminal, but was not recognizable by Chimera, possibly
because of different atomtype names (kindly see attached the snapshot).

Thank you anyways,
Sincerely,
Prathit


On Tue, Jun 29, 2021 at 3:15 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
> > On Jun 28, 2021, at 11:01 AM, Elaine Meng via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Prathit Chatterjee,
> > As the message says, proline 100 is lacking its backbone carbonyl O
> atom.  So you can't add a residue 101 unless you complete residue 100 first.
> >
> > Hide ribbons and display atoms so you can see what you are doing, for
> example, commands something like:
> >
> > ~ribbon
> > display @n,ca,c,o
> > disp :pro
> > focus :98-100.D
> >
> > (1) Select the carbonyl C atom of the proline (Ctrl-click) and use Build
> Structure (in menu under Tools.. Structure Editing).  In that dialog use
> the top menu to change from Start Structure to Modify Structure, choose
> element C, bonds 3, geometry trigonal (because the carbonyl C is
> sp2-hybridized),
>
> one addition:  also choose the option to leave the residue name unchanged
>
> > Apply. That will add 2 hydrogens to the C.  Next select one of those
> hydrogens, choose element O, bonds 1, set atom name to O, Apply.  Now you
> have completed proline by adding the carbonyl O (plus an extra H that you
> can ignore).
> >
> > (2) Now you can use "addaa" to put the alanine after it.
> >
> > If step #1 is too hard for you, another possibility is simply to delete
> the partial proline and then use "addaa" two times, first to add the
> complete proline and then to add the alanine.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Jun 28, 2021, at 12:48 AM, Prathit Chatterjee via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >>
> >> Dear Experts,
> >>
> >> This is regarding adding an ALA residue in the C-terminal of a specific
> protein domain, with CHIMERA.
> >>
> >> I have a protein-complex with multiple domains and chains.
> >> I want to add an ALA residue (101-th position) in the chain D, after
> the 100th residue which is PRO.
> >>
> >> I followed the tutorial and have given the following command in command
> line:
> >>
> >> addaa ala,101 :100.d
> >>
> >> The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D.
> >>
> >> Request you to kindly let me know what the possible solution could be,
> so that I add an ALA residue in the C-terminal of Chain D.
> >>
> >> Thank you in advance,
> >> Regards,
> >> Prathit Chatterjee
> >> t: Chimera-users at cgl.ucsf.edu
> >> Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> >
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