Thanks to Maisam and Paul (answers below) but I still could not see the links in coot after refining.
In coot before refinement, the glucoses are connected, but when I refine, they become disconnected, then if I add a link in coot by doing Extension>Modeling>Add a link, I get disconnected bonds. The LINK I see in pdb as text is for Arg and other residues but not for the sugars Please advise on what I should do to see the sugars connected after refinement, Thank you so much, Remie On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma <[email protected]> wrote: > Hi all, > > I need help creating links between units of sugar (ligands) in the PDB file > before refining so that CCP4 recognizes the sugars are attached. > > I tried the one suggestion I got before Extension > Make a Link, but I get > discontinued bonds instead of full bonds. > > Thanks so much for all your help in advance. > > Remie A dotted line is how Coot represents a LINK. It will not use solid lines for LINKs. You don't need a solid line for Coot and Refmac to consider the residues as bonded. If you examine the output PDB file, you will see a LINK record. Paul. If you open the pdb that Refmac generates ( As text file ) you will see that there is an "R" added to your link and it is "linkR", you need to delete that "R" and press the space button one time to correct for the spacing in your link description, and then coot will show that dotted line. If you want to see a solid line in coot for the links, your sugar molecules should be defined as the residues of the same chain, but to be honest I have never tried that myself. And if you run the refmac, and the pdb that is generated does not show the description of your link that means that the description of your link is not right. Hope this helped. Meisam
