If you are trying to solve an unusual protein structure, here are some hints:

• Treating cysteine bridges: The initial folding step is always done with protonated SG atoms and thus without cysteine bridges. If you know from some other experiment which cysteines are bridged, store the residue numbers in 'cysbridgelist' (see nmr_setdefaults). Alternatively, YASARA can automatically link cysteines that get close enough during the refinement in vacuo.

• Treating metal binding sites with ions: Put the distance restraints involving ions into a second restraint file and run the initial folding step without any ions present. Then add the ions, place them at the center of the protein and then continue with step 2 and both restraint files.

• Treating oligomers: Fold each monomer independently in step 1 and join them together before step 2. If you already know something about their relative orientation and place them accordingly, step 2 will converge much faster. Use sum-averaging and set the 'monomers' parameter to match your data.

• Special residue numbering: If the first residue in the sequence does not have the number '1' in the restraint file, the easiest solution is to renumber the residues using the RenumberRes command, right after the linear peptide chain has been built in nmr_fold by the BuildMol command.