[Chimera-users] [External] Re: adding residues to an existing protein or joining a protein to a small peptide.

[Brody Deming]

Hello Elaine,

Here is a little bit more detail about what we’re trying to do. We are
trying to use Chimera to model a fusion that we constructed in the lab. The
structure we’re working with (pdb: 3pgf) is a complex of a Fab and Maltose
binding protein (MBP). In the lab, we fused the C-terminus of the Fab heavy
chain to the N-termius of MBP with a short linker. In chimera, we would
like to duplicate the structure of the complex, and connect the C-temrinus
of one to the N-terminus of the other. Precisely, we would like to connect
the C-terminus of the heavy chain (Chain H), to the N-terminus of the MBP
(chain A) of the duplicated structure with the short linker.



We have a couple of issues to overcome:

1.     There are a few amino acids missing from the structure at the
C-terminus of chain H, and we would like to add those before connecting to
the N-terminal amino acid (first Lysine) of MBP.

2.     When we try to use the Adda command we can only add a couple of
residues until we get to the following command (adda ser,222 :221.h) at
this point we start getting the message "can't add amino acid, model
already contains residue with sequence '222'".

3.     It would be very helpful we are able to duplicate the entire
structure, and connect the C-terminal of chain H in one structure to the
N-terminal of the MBP (chain A) with the following linker sequence in
between them: DKTHTSGSGA



Thank you again and please let us know if you have any questions or need
additional information.


Thank you,

Brody


Attached is a photo of what we are trying to accomplish using Chimera.


On Wed, Jun 3, 2020 at 12:10 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
> -------
>
> Hi Brody,
> To say much of anything, we would generally need more details, such as:
> what exactly you are trying to do (e.g. what kind of residue on which end
> of what structure), the specific commands or tool steps that you used, and
> what you mean by "having trouble,."
>
> In case you didn't already know, there is a command "addaa" described
> here, including an example:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
>
> 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 2, 2020, at 6:19 PM, brody deming <demingb at iu.edu> wrote:
> >
> > Hello,
> >
> > I am a Student at Indian University South Bend and I am doing some
> modeling using Chimera. I am having trouble trying to add residues to an
> existing protein I am working with. I am wondering if you had any advice
> for how to do this.
> >
> > Thank you,
> > Brody
>
>
>
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