| Model search |
Sequence-based search (FASTA) |
Sequence-based search, domain identification and alignment generation (phmmer, HHpred) |
| Domain identification (SCOP) |
| Alignment generation (ClustalW, MAFFT) |
| Search-model preparation |
Generation of mixed models based on sequence alignment (CHAINSAW, MOLREP) |
Graphical search-model interaction (CCP4mg) |
| Single untruncated ensemble (Superpose) |
Generation of mixed models based on sequence alignment (Sculptor, CHAINSAW, MOLREP) |
| Multiple truncated ensembles (using GESAMT or AMPLE) |
| Molecular replacement |
MR (Phaser, MOLREP) |
MR (Phaser, MOLREP) |
| Refinement |
30 cycles of restrained refinement (REFMAC) |
100 cycles of restrained refinement with jelly-body restraints (REFMAC) |
| Density modification |
Phase improvement for target data better than 1.7 Å resolution (ACORN) |
Phase improvement for target data better than 2.4 Å (SHELXE) or 1.7 Å (ACORN) resolution |
| Model building |
|
Polyalanine main-chain tracing (SHELXE) |
| Full model building (ARP/wARP and Buccaneer) |
