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

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 26 13:28:50 PDT 2020

Hi Brody,
The structure PGF has waters, glycerol, etc. and they have residue numbers and belong to chain H. When you get a message like that you could "display :222.h" and "focus :222.h" or something like that to see what it's complaining about.... in this case a glycerol (GOL 222.H).  If you don't care about residues like that you can just delete them before you start building.  These commands work fine for me:

open 3pgf
delete ~protein
display @n,ca,c,o
addaa asp,217 :216.h
addaa lys,218 :217.h
addaa thr,219 :218.h
addaa his,220 :219.h
addaa thr,221 :220.h
addaa ser,222 :221.h
addaa gly,223 :222.h
addaa ser,224 :223.h
addaa gly,225 :224.h
addaa ala,226 :225.h
rlabel :215-226.h

(~protein means everything that's not protein) Then you can open the structure that you want to stick on the end (if it's also 3pgf, just open it again).  You have to open it again because it needs to be in a separate model from the first one for the "join models" step that is next.  

open 3pgf
delete ~protein
disp @n,ca,c,o

Also if you don't care about the chains other than the ones you will be joining, then clean up first by deleting them.  Assuming the first model is #0 and the second is #1,

delete #0 & ~ :.h
delete #1 & ~ :.a
(delete everything in #0 that isn't chain H, delete everything in #1 that's not chain A)

Join models is a section in Build Structure (in Tools menu under Structure Editing). In that "join models" panel, you'd choose the peptide bond option.  To be able to select the proper backbone atoms for the join, you'd need to hide ribbon and show backbone atoms, as done in the example commands.

An alternative approach would be completely with Build Structure, not using addaa:

(1) in the "start structure" section of Build Structure, choose the peptide option, enter sequence of just the linker part to build it as a separate model
(2) open the structures that will be on either end of the linker.  If it's the same structure, just open it twice. (again can delete extra chains from everything to clean up)
(3) in the "join models" section of Build Structure, first join the preceding structure (let's call it chain1) to the linker, and then join the following structure to the new model you just made of chain1-linker. You'd use the peptide bond option mentioned above.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 26, 2020, at 11:13 AM, Brody Deming <demingb at iu.edu> wrote:
> 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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