Date: 7 February 2012 21:44
Hi folks,
I have an intriguing problem. I'm trying to generate a cif file for a macrocyclic peptide (of the likes in pdb1d4k). They are cyclic tripeptides units. I can generate a pdb or mol2 file easily. I have used PRODRG to generate a .cif file and Coot read thjis in nicely. However, as it is cyclic one cannot adjust the dihedral angles. I have previously done this using CNS where you can break the tricyclic peptide into residues and generate parameters to specify bonds/links between the residues (which allows this kind of movement). I can't come up with a way to do this without using CNS. I have looked ta J-ligand which allows for one link "between" two separate residues which precludes a macrocycle. I have looked at sketcher within CCP4 which reads the pdb files but I don't believe this can be done here. Within Coot I can refine the whole ligand but not certain components.
Any suggestions greatly appreciated . ( I may stick to coot refinement with fixed atoms at this stage)
Regards
Joel
_________________________________
Joel Tyndall, PhD
----------
From: <Herman.Schreuder
----------
From: Garib N Murshudov
----------
From: Joel Tyndall
Hi Garib,
Thanks for that (and thanks Herman). How do I declare a non-natural amino acid a peptide? My ligand contains two peptidic cycles (non-N to C) where the side chains are cyclised. I think I'll be able to use several linbk records for the connections but the non-natural amino acid are complicating the issue
----------
From: <Herman.Schreuder
This comment has been removed by the author.
ReplyDelete