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Re: [ccp4bb]: maintain conformation of R3N(+)H in refmac
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Dirk Reinert wrote:
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> Dear all,
> I am refining a structure that contains an inhibitor featuring a R3N(+)H group
> (I am quite certain that the N is protonated). The problem is that I do not
> know how to tell refmac to keep the H whith the result that I get a flat R3N
> after refinement. The structure of the inhibitor is not in the standard
> library so I had to create my own description with the monomer library
> scetcher (where I used an energy minimised pdb of the inhibitor with Hs).
> what am I doing wrong? Any suggestions are highly appreciated.
In sketcher if you define oxidation of N as +1 (that is on the right of atom
names) then you should get tetrahedral Nitrogen.