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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