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
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