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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. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1