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@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@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
