I am trying to append four residues (MQFF) to the N-terminus (G) of a protein fragment, and whenever I generate the 4-residue peptide and fuse the appropriate atoms together, it always reads MQFGF instead of MQFFG, like the fragment has somehow invaded the N-terminus instead of latching to the end. When I change views and select individual residues there's a conspicuous gap. I fixed this issue by appending FF, then Q (because F then F resulted in some wonky behavior too, and QFF resulted in QFGF), but I cannot seem to add M (by itself) without getting QMFFG. Obviously, I want MQFFG. What's wrong here, and how can I append correctly? I'm using the same command every time (fuse (pk2),(pk1) ; 2 then 1 is just a quirk of my selections and definitely not the issue).
Elsewhere in my project, I'm trying to fuse two large fragments together, but no matter how I specify my selections, they are not lining up correctly in the sequence display. I want to link ...MRDE to KRTH... To form ...MRDEKRTH... but when I fuse it always puts the wrong ends with each other (i.e. the end of fragment 2 with the beginning of fragment 1 as opposed to the end of fragment 1 with the beginning of fragment 2 as desired). However, it fuses properly visually. Also, the sequence displays it as two objects stitched together, and not as one continuous object like when I added the 4 residues to my first fragment. There's a standard numbering scheme for the first fragment, then a double slash, then it restarts with the scheme associated with the second fragment. Is there anyway to make it so the fused fragments read as one object with a seamless residue sequence?