 |
 |
Dear lei feng, The cif file (GLC-b-D.cif in the Refmac dictionary) is indeed for just one monomer. Links are specified in the list/mon_lib_list.cif file. There you will find a description of the BETA1-4 linkage. You will see that O4 is linked to C1 of the following residue - and that if you examine the chem_link for BETA1-4 you will notice that O1 is deleted. You need to make sure that the atoms in your PDB file correspond (not all PDB models do, e.g. 3BMW does not). Once you have consistent atoms in the PDB file, the glycosidic linkage will be detected by Coot and just work [1]. You do not need Sketcher, libcheck, extra cif files or extra LINK lines added to your PDB file. Paul. [1] I should be clear that it will "just work" with tandem unbranched carbohydrates (as is the case in maltoheptaose). Petr Kolenko wrote: > Hi Lei. > As I expect, you use REFMAC for structure refinement. This link should > help you to connect in principle any atoms between residues (or ligands > as well). > > http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_link > > You can also find many examples of different LINKs in the PDB records. I > would prefer the most similar ones. ;) > > Best wishes, > Petr > > > Petr Kolenko > [log in to unmask] > protein.awardspace.com > > > > lei feng wrote: > >> Hello Carlos >> >> thanks for your kindly reply. I think the cif file ( GLC_mon_lib.cif >> ) is only for one glucose molecule, it can not regulate the bond >> between two glucose units, that is why they break apart in the real >> space refinement. >> >> in the pdb file , different glucoses are different molecules, I do >> not know how to generate a cif file to give regulation on bond between >> glucose units. If we can make this cif file , is it the same as >> GLC_mon_lib.cif? >> Thanks a lot for you help . >> >> Yours >> Lei >> >> >> > Date: Wed, 5 Nov 2008 17:23:58 -0600 >> > From: [log in to unmask] >> > To: [log in to unmask] >> > Subject: Re: [ccp4bb] sugar ligand refinement in coot >> > >> > Lei, >> > >> > If your cif file isn't complete, you can load your pdb GLC in >> Sketcher in ccp4 suite and generate a cif file. When you have your >> cif, import your cif file inside coot. >> > >> > Carlos >> > >> > >>> lei feng <[log in to unmask]> 11/05/08 4:08 PM >>> >> > >> > hello everyone >> > >> > can anyone help me with sugar ( say maltoheptaose) refinement in coot? >> > >> > I use the pdb file with " GLC " name , it always breaks apart into >> discountinuous glucose when I try to use real space refinement , I >> believe that is because there is no restraint with regarding to bond , >> whatever in cif file. >> > >> > I know I could give it a unique name , say G7 and substitute the " >> GLC "it in the pdb file, make a new cif file and refine it , it will >> not break apart again. But , when I deposit the structure in the >> future , it is allowed? It seems everyone working with sugar ligands >> are using " GLC" . how did they work in refinement ? >> > >> > Thanks for any suggestion. >> > >> > lei Feng