Dear Remie,

For reasons that probably only Garib understands, Refmac still uses LINKR instead of LINK to link atoms. However (at least for Refmac) both LINK and LINKR should work.

After a lot of complaining in the past (also from my side), the handling of carbohydrates in Refmac is ok. I just did some tests with N-linked carbohydrates (NAG, MAN): after using the Make Link option in coot and saving the file, there were regular LINK records, created by coot. After running refmac from within coot and saving the files, the LINK records were converted (perverted?) to LINKR records. However, they did not disappear and after restarting coot and loading the file again, they were still there. Also my version of pymol recognizes both LINK and LINKR records, since the connections are shown when I load the files before and after running refmac.

Some suggestions: check that you are using recent versions of coot, refmac and pymol. Older versions may have problems. I don't know how you construct your carbohydrates, but if you get the monomers, you have to delete an oxygen atom in the link (in my case the O1 atom). Make also sure that your starting geometry is acceptable. Just doing a real space refinement usually works well, but sometimes the carbohydrate crashes into the protein density and you will have to manually fit the sugar as good as possible. Some of the older files in the PDB may have distorted carbohydrates, so here it is probably best to build the carbohydrates again from scratch (get monomer, delete linking oxygen) etc.    

Good luck!
Herman






-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Remie Fawaz-Touma
Gesendet: Mittwoch, 28. Mai 2014 16:13
An: [log in to unmask]
Betreff: [ccp4bb] Refmac5

Hello everyone,

When I refine in CCP4 a structure with Glc units attached every few of them as a ligand and there are several of them in the same file, I start off with a PDB that shows the LINK records between the GLC units as LINKR because I add the links by > Extensions > Modelling > Make Link (2 atoms) in COOT. 

What does LINKR mean? why not just LINK?

More importantly, when I refine, the output PDB file does not contain the LINK records, why do they go away? and in PyMol I see only GLC that are close enough to make a covalent bond stay connected, the others become detached, in CCP4 they all show detached, but if I do a real space refinement for those sugars of the same ligand in the output file, they come close together and attached?

Any suggestions?

Thank you very much in advance.

Remie