Dear Leo, Just in case, you have to delete the oxygen from the carbon making the covalent link in the sugar you are adding to the chain (in the direction starting from the Asn or Ser). This is usually the O1. Then you make a link between this carbon and the connecting O or N atom. I usually do a real space refinement of the single sugar unit and I continue rebuilding until the atoms to be connected are within reasonable distance to make the link after this real space refinement. You may have to rebuild the Asn or Ser as well. In my experience, if the link is correctly specified and the sugar is correctly modeled, it will refine correctly without having to add or generate an additional cif file.
Good luck, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Bärbel Blaum Gesendet: Freitag, 5. September 2014 08:49 An: [email protected] Betreff: Re: [ccp4bb] How to make covalent bond between sugar monomers? Hi Leo, you should not need an additional cif file for coot but you might need to generate one for reciprocal space refinement. If you use REFMAC it might 'fail' in the first attempt with the message 'new ligand encountered' or something similar. It will, however, generate a single cif file for the sugar if it recognizes the monosaccharides and the glycosidic linkage you have created in coot, using the descriptions from the REFMAC library. You can then look at this cif file and provide it for future refinement runs in REFMAC. It is a good idea to keep checking if the glycosidic bond is identified correctly and restrained accordingly in every REFMAC run after you introduced the ligand/glycosylation. I find it a lot harder to achieve correct sugar refinement with phenix, although elbow should techically be able to create a cif file for sugars just like REFMAC. The prodrug server is a bad idea, as pointed out, because the library restraints for sugars are not used if the sugar rings are not identified with the correct three letter abbrevations in your pdb file. If you have a larger oligosaccharide and good density it might be easiest to start by getting a similar sugar model from a deposited pdb file. Place this molecule in your sugar density using rigid body refinement, then start to manipulate single rings from the template so that they fit your density best. Often this is a matter of rotating the individual rings around their glycosidic bonds. When you try this procedure be aware that there are lots of distorted sugar rings in the pdb, so make sure you start from a good template. Good luck, Baerbel Zitat von Lie Ma <[email protected]>: > Thank you, Paul. > > And do I need to provide additional cif file which describe the bond? > > Leo > > On Sep 4, 2014, at 2:23 PM, Paul Emsley <[email protected]> wrote: > >> On 04/09/14 19:06, Lie Ma wrote: >>> Hello all, >>> >>> I am trying to make a model of an oligosaccharide which contains >>> several sugar monomers. I obtained the monomers from coot library >>> and put them into the electron density. But I don't know how to make >>> covalent bond between these monomers. >> >> If you are using Coot, you can use Extensions -> Modelling -> Make Link. >> >> If you sugar monomers are reasonably placed Coot's Sphere Refine will >> determine the correct link types on the fly (it doesn't believe >> what's in the PDB file). >> >>> >>> I tried to use PRODRG to generate a model and it gave me one big >>> ligand consisting of several monomers. >> >> Yes, that's not the way to do it... >> >>> However, what I want is to have a chain contains several monomers, >>> and each monomers acts like a residue. >> >> Indeed. >> >> >> Paul. >> > -- Bärbel Blaum, Ph.D. Interfakultäres Institut für Biochemie (IFIB) Hoppe-Seyler-Strasse 4 D-72076 Tübingen Germany +49 70 71 29 73 375
