On 04/11/2019 17:06, Pavel Mader wrote:
> Hi Paul,
>
> thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids,
> the side chains of which are linked by click chemistry... I know how to make modified amino acids that will
> make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent
> link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain).
OK...
> I was trying
> to solve the issue by making a CONECT record in the pdb file,
That's not the way to do it.
> but Coot ignored it.
Indeed.
> LINK "sort of" worked,
But not really, right?
> but it was not possible to control the geometry (bond length and angles), often the real space refinement
> simply "explodes" probably in a attempt to avoid clashes.
Yeah...
> My current workaround is to make a cif file for the whole 15 AA long polypeptide
Blimey!
> (the bonds and angles now behave more or less as expected), but I don't
> consider this as a good general practice for building long polypeptide chains...
Hmm! Your scepticism is well placed, I feel.
The way to do it is to use the Coot (Modules -> CCP4 -> Acedrg Link) or CCP4i2 interface (Ligands -> Make a
Link (?)) so that Acedrg is used to make a link between the specified atoms of the specified residue types
(monomers).
Note: to self: make a YouTube vid to explain how to do this...
Paul.
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