Using your favorite editor, you can copy the LINK record from the pdb file generated by Coot and paste it into the pdb file produced by Phenix. You can also make a script to do this. This is what I did during the time LINK records were not properly handled by coot, refmac and buster.
Best regards, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry Rodionov Gesendet: Donnerstag, 21. November 2013 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Dealnig with O-linked mannose Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions->Modelling ...->make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry
