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On 26 December 2011 03:25, Dialing Pretty <[log in to unmask]> wrote: > Dear All, > > You see the part labelled "D and "LARGE" in the attached image is the part > for the last residue in a chain, however it localizes in the red part. If I > can change the part labelled "D" and "LARGE" into the part labelled "F", the > red should have disapeared. > > But after several rounds of try by Coot, I have not make the above exchange. > > Will you please give me your suggestions on how to change the part labelled > with "D and "LARGE" into the part labelled by "F" with Coot or with some > other methods? > > Cheers, > > Dialing This is almost certainly doable in coot, with a bit of fiddling/practice. I would try to real-space-refine the terminal Glu (perhaps together with the Lys), and over-drag one of the side chain atoms into the blob of interest (hold Ctrl and drag a single atom further than its desired destination and it will pull the other atoms along once Ctrl is released). In some cases it can be easier to start with regularisation instead of real space refinement. There are other methods too, like editing torsion angles (both single and multi-residue, I think) and the rotate-translate option can come handy too. Just keep poking at those pesky residues -- it might take a couple of tries and some patience. It might actually be the main chain continuing into the area labeled F, with little density for the side chain, but it is hard to judge from a 2D image.