| Program | Task | Module | Comment |
|---|
| AMoRe |
AMoRe |
Molecular Replacement |
See AMoRe |
| ARP/wARP |
Run ARP |
Refinement |
See ARP |
| Cad |
Merge MTZ Files (Cad) |
Reflection Data Utilities |
Program also part of "Convert to MTZ & Standardise" Task. See
CAD |
| Combat |
Import Unscaled Data |
Data Reduction |
See Combat |
| Coordconv |
Convert Coordinate Formats |
Coordinate Utilities |
See Coordconv |
| Detwin |
Treat Twinned Data |
Data Reduction |
See Detwin |
| dm |
Run DM |
Density Improvement |
See Kevin's dm Workshop |
| Dtrek2mtz |
Import Scaled D*trek Data |
Data Reduction |
See d*TREK2MTZ
and the
d*TREK program documentation |
| Ecalc |
Prepare Data for HA Search |
Experimental Phasing |
Combined with Revise and MTZ2various to prepare data for experimental
phasing. See Ecalc |
| Extend |
Run FFT |
Several |
Hidden program. See Extend |
| F2mtz |
Convert to MTZ & Standardise |
Reflection Data Utilities |
Task also called "Import".
See F2MTZ |
| FFFear |
FFFear - Fragment Searching |
Model Building |
Output coordinates should be seen as Calpha-trace; external model building
necessary |
| FFJoin |
FFJoin - Merge fragments |
Model Building |
Output Calpha-trace to be built upon externally |
| FFT |
Run FFT - Create Map |
Map & Mask Utilities |
Generate map with FFT, optionally Extend to cover molecule, convert to alternative
format. See FFT |
| FFT for Patterson |
Generate Patterson Map |
Experimental Phasing |
Run FFT to generate Patterson map, generate 2D plot of Harker sections. See
FFT |
| FFT for native Patterson |
Analyse Data (Patterson) |
Molecular Replacement |
Run FFT to generate native Patterson map to check for pseudo-translation. See
FFT |
| Fhscal |
Scale Datasets |
Experimental Phasing |
Choose between Fhscal and Scaleit, see
scaling. See also
Fhscal |
| Freerflag |
Convert to MTZ & Standardise |
Reflection Data Utilities |
Task also called "Import", see
FreerUnique. See also
Freerflag |
| LSQKAB |
Superpose Molecules |
Coordinate Utilities |
Alternative to Top. See LSQKAB |
| Mapman |
Run FFT - Create Map |
Map & Mask Utilities |
Hidden Program. Non-CCP4; see
Uppsala Software Factory
- MAPMAN Manual |
| Mapmask |
Edit/Rotate Maps & Masks |
Map & Mask Utilities |
See Mapmask |
| Mapmask |
Run FFT - Create Map |
Map & Mask Utilities |
Hidden Program. Extend map to cover molecule. See
Mapmask |
| Mapmask |
Generate Patterson Map |
Experimental Phasing |
Hidden program. Reorder map axes. See
Mapmask |
| Maprot |
Map Averaging |
Map & Mask Utilities |
For averaging and correlation. See
Maprot |
| Maprot |
Edit/Rotate Maps & Masks |
Map & Mask Utilities |
For interpolation&rotation. See
Maprot |
| Matthews_coef |
Cell Content Analysis |
Coordinate Utilities |
See Matthews_coef |
| Mbkall |
Run FFT - Create Map |
Map & Mask Utilities |
Hidden program. |
| Mlphare |
Run Mlphare |
Experimental Phasing |
See MLPHARE |
| Modeller |
Edit Protein Structure |
Molecular Replacement |
Non-CCP4 program. See
Sali Lab at The Rockefeller University |
| Molrep |
Molrep - auto MR |
Molecular Replacement |
See Molrep |
| Mtz2various |
Convert from MTZ |
Reflection Data Utilities |
Task also called "Export". See
MTZ2various |
| Mtz2various |
Prepare data for HA Search |
Experimental Phasing |
Combined with Revise and Ecalc to prepare data for experimental phasing. See
MTZ2various |
| Mtzdmp |
|
|
Hidden program, runs when View button is clicked for MTZ files (see
View).
See also MTZDUMP |
| Mtzutils |
Convert to MTZ & Standardise |
Reflection Data Utilities |
Hidden program; task also called "Import". See
MTZutils |
| Ncsmask |
Create/Edit Masks |
Map & Mask Utilities |
See NCSMASK |
| NCSref |
NCS Phased Refinement |
Refinement |
Combination of 'dm' and REFMAC, with a bit of LSQKAB and maybe more,
to have a handle on the start of refinement in the case of ncs being present. |
| NPO |
Generate Patterson Map |
Experimental Phasing |
See NPO |
| Overlapmap |
Map Correlation |
Map & Mask Utilities |
Used in conjunction with SFALL to calculate map correlation. See
Overlapmap |
| Pdbset |
Edit PDB File |
Coordinate Utilities |
See PDBSET |
| Peakmax |
Generate Patterson Map |
Experimental Phasing |
See Peakmax |
| Prmap |
|
|
Hidden program, runs when View button is clicked for map files. See
PRMAP |
| PROCHECK |
Run SFCHECK&PROCHECK |
Refinement |
See PROCHECK |
| Protin |
Protin Restraints |
Refinement |
Program runs at start of actual refinement program. See
Protin |
| Rantan |
Rantan - Direct Methods |
Experimental Phasing |
See RANTAN |
| Rebatch |
Sort/Reindex MTZ Files |
Data Reduction |
See Rebatch |
| Refmac |
Run Refmac |
Refinement |
Task includes running Protin. Also involved in NCSref. See
Refmac |
| Refmac5 |
Run Refmac5 |
Refinement |
See
Refmac5 |
| Reindex |
Sort/Reindex MTZ Files |
Data Reduction |
See REINDEX. See also
Reindex. |
| Reindex |
Reindex Reflections |
Reflection Data Utilities |
This is the option to use for 'standard' (i.e. non-multi-record) MTZ files.
See REINDEX. |
| Revise |
Prepare Data for HA Search |
Experimental Phasing |
Combined with Ecalc and MTZ2various. See
REVISE |
| Rotaprep (now called Combat) |
Import Unscaled Data |
Data Reduction |
Now called Combat. See
COMBAT |
| RSPS |
Real Space Patterson Search |
Experimental Phasing |
See RSPS |
| Scala |
Scale Experimental Intensities |
Data Reduction |
See Scala |
| Scaleit |
Scale Datasets |
Experimental Phasing |
Choose between Scaleit and Fhscal, see
scaling. See also
SCALEIT |
| Scalepack2MTZ |
Import Scaled Denzo Data |
Data Reduction |
See Scalepack2MTZ |
| Sfall |
Create Input SFs from Model |
Molecular Replacement |
Combined with Ecalc to prepare 'map' for use in molecular replacement. See
SFALL |
| Sfall |
Map Correlation |
Map & Mask Utilities |
Combined with Overlapmap. See SFALL |
| Sfall |
Calculate Fs & Phases |
Reflection Data Utilities |
See SFALL |
| SFCHECK |
Run Sfcheck & Procheck |
Refinement |
See SFCHECK |
| Sftools |
Edit MTZ File (Sftools) |
Reflection Data Utilities |
See SFTOOLS |
| Shelx |
SHELX - Heavy Atom Search |
Experimental Phasing |
Non-CCP4 program. See
THE SHELX HOMEPAGE |
| SIGMAA |
Sigma-A |
Reflection Data Utilities |
Interface to SIGMAA not complete/finished |
| Solomon |
Run Solomon |
Density Improvement |
Includes option to truncate density. See also
Solomon |
| Sortmtz |
Sort/Reindex MTZ Files |
Data Reduction |
See SortMTZ |
| Top |
Superpose Molecules |
Coordinate Utilities |
Alternative to LSQKAB. See Top |
| Truncate |
Convert Intensities to SFs |
Data Reduction |
Be careful with LABIN/LABOUT. See
Truncate. Also part
of the 'Import Scaled Denzo Data' task. |
| Uniqueify |
Convert to MTZ & Standardise |
Reflection Data Utilities |
Task also called "Import", see
FreerUnique. See also
Unique |
| Vectors |
Generate Patterson Map |
Experimental Phasing |
See Vectors |
| warpNtrace |
Run warpNtrace |
Model Building |
Direct from author(s) |
| XtalView/xfit |
XtalView/xfit |
Model Building |
See XtalView |
