Dear Emmanuel, Is the modified residues are really new, you can make restraint files with jligand or acedrug (both in CCP4). Make sure the backbone atoms have the same names as in standard amino acids. Now open de cif-file(s) in a text editor and set the residue type to 'peptide' (you can use ALA.cif from ccp4 as an example). If your residues are sequentially numbered, then Refmac should detect the LINKs automatically. Coot may do that as well.
HTH, Robbie -----Oorspronkelijk bericht----- Van: "ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ" <[email protected]> Verzonden: 20-1-2015 16:55 Aan: "[email protected]" <[email protected]> Onderwerp: [ccp4bb] fitting peptide with non-standard and standard amino acids Dear All, I wonder if you could help me with this. I am trying to do some regularisation/real space refinement of a ligand with Coot. The ligand is a pseudopeptide with two non-standard aminoacids, followed by several standard ones. I assume that to do this correctly, I would need a cif file that specifies the two non-standard aa's plus the links between these two and between second and third (which is a standard one). When trying to generate a cif with a program such as eLBOW (using a pdb as the starting reference), each of the non-standard aa's gets a cif of its own, and the third, standard one, is ignored, meaning that there are no specified links between the first two (non-standard) and even less between second (non-standard) and third (standard). Coot of course keeps each aa as it should be, but breaks up the peptide chain completely. Could you direct me how to built a cif that includes such bond specifications, starting from a reference pdb or otherwise? Is there an altogether different way of getting Coot to do what I want? Many thanks, Emmanuel Dr. Emmanuel Saridakis Researcher C Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE
