| Data import |
Import of project data: merged and unmerged MTZ files, PDB/mmCIF files, sequence files. The file type is recognized automatically and all data are arranged in data sets at the metadata level, such that all subsequent jobs can operate with data sets rather than explicit reference to files. For example, MTZ files can be logically split into several data sets, PDB files may be split into chains, and files with multiple sequences are split into individual sequence entities. |
| Convert to structure |
Association of coordinate and density/phase data, usually after data import. In jsCoFE, coordinates and density maps are associated to optimize data flows. |
| POINTLESS/AIMLESS |
POINTLESS/AIMLESS pipeline for scaling and merging data |
| Reindex |
Changing the space group, usually required in the case of reflection-data enantiomorphism |
| AsuDef |
Definition of the asymmetric unit and Matthews analysis |
| BALBES |
Automatic molecular replacement with BALBES
|
| MoRDa |
Automatic molecular replacement with MoRDa
|
| MR ensembling from sequence |
Making MR model ensembles through sequence searches in the PDB |
| MR ensembling from coordinates |
Making MR model ensembles from given coordinate data |
| MOLREP |
Molecular replacement with MOLREP
|
| Phaser-MR |
Molecular replacement with Phaser
|
| SHELX-MR |
After-MR autotracing with SHELXE
|
| CRANK2 |
Automatic experimental phasing with CRANK2 (SAD, MAD, SIRAS) |
| SHELX-auto |
Automatic experimental phasing (SAD, MAD, SIRAS) using the SHELX suite |
| SHELX-Substr |
Heavy-atom location with SHELXC/D
|
| Phaser-EP |
Experimental phasing with Phaser
|
| Parrot |
Density modification with Parrot
|
| REFMAC |
Macromolecular refinement with REFMAC
|
| LORESTR |
Low-resolution refinement pipeline |
| Buccaneer-MR |
Automatic model building with Buccaneer after MR |
| MakeLigand |
Making ligand structure and restraints with AceDRG
|
| FitLigand |
Fitting ligand with Coot
|
| FitWaters |
Fitting water molecules with Coot
|
| Zanuda |
Space-group validation with Zanuda
|
| GESAMT |
Pairwise and multiple structural alignment and structural searches in the PDB with GESAMT
|
| PISA |
Oligomeric state and interface analysis with PISA
|
