Uppsala Software Factory - All programs

1. ALPHABET: not documented or released
2. AVE for single-crystal averaging
3. AVEPDB to average models
4. CELLO to play with your cell
5. COMAP to combine maps during multiple-crystal averaging
6. COMDEM to combine multiple domain maps
7. CRAVE to auto-generate a C-shell script to do N cycles of averaging over M crystal forms, each with or without NCS
8. CT2HET to find hetero compounds in the PDB using only atom type and connectivity information (using the hetero-compound collection OMAC/hetero.pdb)
9. DATAMAN to manipulate reflection datasets
10. DCUP to do quick calculations during data-collection
11. DEJANA: see DEJAVU
12. DEJAVU to find motifs and to recognise other proteins with a similar fold (includes documentation for DEJANA, PRO1, PRO2 and POST)
13. ESSENS to do real-space searches for fragments (e.g., helices) or molecules
14. FITAL: not documented or released
15. FLOOD to fill a cavity with water molecules
16. HETZE to check the geometrical quality of hetero compounds (before or after refinement)
17. IMP to improve NCS operators
18. LSQMAN to superimpose and analyse multiple models and/or molecules
19. MAMA to manipulate masks
20. MAPFIX add spacegroup and symmetry operators to a CCP4 map
21. MAPMAN to manipulate maps
22. MAPPAGE: not documented (obsolete; use MAPMAN instead)
23. MAPROP to produce maps of various properties
24. MAVE for multiple-crystal averaging
25. MKSPAZ: see SPASM
26. MOLEMAN to do all sorts of things with/to PDB files (obsolete except for a few arcane options; use MOLEMAN2 instead !)
27. MOLEMAN2 to do everything you used to do with MOLEMAN, but: better, stronger, faster !
28. NCS6D to find NCS operators
29. NHANCE: not documented
30. O2D to make 2D plots
31. ODBM to analyse O datablocks (ODBMAN offers many more options !)
32. ODBMAN to analyse O datablocks
33. ODLEDIT: not documented
34. OOPS to scrutinise your model and generate rebuilding macros for O
35. OST: not documented (superceded by SOD)
36. PACMAN to check packing after Molecular Replacement
37. PDB2CT: not documented
38. POST: see DEJAVU
39. PREDIC: not documented or released
40. PRO1: see DEJAVU
41. PRO2: see DEJAVU
42. PROF to generate electron-density profiles (only in Uppsala at present)
43. QDB is a program to query a database containing statistics and quality information for 476 X-ray protein structures
44. RIGOR to find predefined motifs from other structures in your model
45. RMSPDB to analyse multiple models (LSQMAN does this much better !)
46. SEAMAN to generate search models for Molecular Replacement
47. SOD to generate O datablocks from (aligned) sequences
48. SOLEX to extract the best solutions from ESSENS runs (and to attempt to auto-trace helices and strands)
49. SPANCSI investigate if your NCS-related molecules have very different average temperature factors, and if so, take special measures during averaging
50. SPASM to find motifs of main and/or side chains (includes MKSPAZ documentation)
51. VOIDOO to find cavities and analyse volumes
52. XPAND to expand molecules under NCS and/or spacegroup symmetry
53. XPLO2D does "stuff" to X-PLOR input or output files; most popular for its option to auto-generate topology and parameter files for hetero-entities in X-PLOR