Macromolecular CrystallographySoftware
You will find below the description of software for crystallography as well as sample input scripts.
Please note: Before launching a program, you need to type prepare [program_name] to set up the proper environment. Click the link "prepare info" to know more about prepare.The link also provides information on the software packages available.
Strategy |
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| BEST | Sasha's and Gleb's data collection strategy | Manual |
| DNA | available at X13 for data collection strategy, indexing and integration | Manual |
Data Processing |
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| HKL 2000 | HKL 2000 def.site files for our beamlines download | get def.site |
| HKL Package | Denzo and Scalepack | example input |
| XDS | Wolfgang Kabsch's processing program | example input |
| MOSFLM | York's favourite | |
| d*TREK | ||
| scerror | No description, but a very handy script for adjusting scalepack's error model! | example input |
| chooch | Processing of the fluorescence scan for MAD, determination of f" and f' | example input |
Structure Solution |
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| SOLVE | For MAD, SAD, SIRAS, MIRAS ... | example input |
| ReSOLVE | Trace your protein | example input |
| (auto)SHARP | Powerful phase determination for MAD, SAD .. | |
| SHELX | SHELXD for substructure soluti | example input |
| CNS | CNS-solve, molecular replacement | |
| Amore | CCP4 compatible, automatic molecular replacement | example input |
| TNT | ||
| SnB | ||
| MOLREP | Molecular replacement package | |
| CCP4 | List of all CCP4 programs | |
| ARP/wARP | Inital model building and tracing | |
| Auto-Rickshaw | Our automated structure solution pipeline | |
Refinement |
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| Refmac5 | Structure refinement | example input |
| X-Plor | CNS pre-cursor | |
| CNS | CNS-refine for structure refinement | |
| SHELX | SHELXL for refinement, SHELXPRO for conversion tools. | |
| CCP4 | List of all CCP4 programs | |
| ARP/wARP | Iterative model and solvent building, ligand search | |
Graphics |
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| O | Manual model building | Manual |
| Turbo Frodo | O's counterpart | |
| XtalView | Building and visualisation | |
| Coot | Model building, easy to learn | |
Visualisation |
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| Molscript | Excellent structure drawing program: ribbon representation, ball-and-stick, CPK ... | example input |
| Raster3D | Rendering of pictures output from Molscript | |
| RasMol | Also a structure viewer | |
| GRASP | Surface and properties representation | |
| XtalView | Nice electron density pictures | |
| Pymol | ||
Various Tools |
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| Uppsala SW Factory | Anything O-related, MAPMAN, MOLEMAN, etc. | |
| Alscript | Sequence alignments to postscript | example input |
| CCP4 | List of all CCP4 programs |