[phenixbb] How we process the change of the conformation of the terminal residue in this situation

Timothy Springer springer at idi.harvard.edu
Mon Dec 26 08:43:18 PST 2011

Does the part at D connect to the polypeptide to right through region F? If so you can move each residue so its backbone is in density and spaced appropriately to connect structurally, and use regularize to connect. You have to rebuild the part on right, too. On the right, put the mainchain, not sidechain of that acidic residue into density.  Are there any structural homologues of what you are building? Search pdb sequences for sequence homology and superimpose. They can give good hints for rebuilding 
I am amazed you have gotten so far with this with bulletin board help. Is there anyone nearby you could go to? Having personal guidance would be very helpful with coot. 

On Dec 25, 2011, at 9:25 PM, Dialing Pretty 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
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