Uppsala Software Factory - All programs

This is an alphabetic (I hope) list of all of Gerard's programs. If you don't know what program to use to solve your particular problem, try the inverted index.
  1. ACONIO to split PDB files with alternative conformations so they can be used in O
  2. ALPHABET: not documented or released
  3. AVE for single-crystal averaging
  4. AVEPDB to average models
  5. CELLO to play with your cell
  6. COMA to find NCS mask using local correlation maps
  7. COMAP to combine maps during multiple-crystal averaging
  8. COMDEM to combine multiple domain maps
  9. CRAVE to auto-generate a C-shell script to do N cycles of averaging over M crystal forms, each with or without NCS
  10. CT2HET to find hetero compounds in the PDB using only atom type and connectivity information (using the hetero-compound collection OMAC/hetero.pdb)
  11. DATAMAN to manipulate reflection datasets
  12. DCUP to do quick calculations during data-collection
  13. DEJANA: see DEJAVU
  14. DEJAVU to find motifs and to recognise other proteins with a similar fold (also includes documentation for DEJANA)
  15. ESSENS to do real-space searches for fragments (e.g., helices) or molecules
  16. FINDNCS to find NCS operators in sets of atoms
  17. FITAL: not documented or released
  18. FLOOD to fill a cavity with water molecules
  19. GETSSE to generate an SSE file for DEJAVU from a PDB file of a protein
  20. HETZE to check the geometrical quality of hetero compounds (before or after refinement)
  21. IMP to improve NCS operators
  22. LIGCOM to check and compare the geometry of hetero compounds
  23. LSQMAN to superimpose and analyse multiple models and/or molecules
  24. MAKRIG: see RIGOR
  25. MAMA to manipulate masks
  26. MAPFIX add spacegroup and symmetry operators to a CCP4 map
  27. MAPMAN to manipulate maps
  28. MAPPAGE: not documented (obsolete; use MAPMAN instead)
  29. MAPROP to produce maps of various properties
  30. MASKIT to find cross-crystal averaging mask using local correlation maps
  31. MAVE for multiple-crystal averaging
  32. MKSPAZ: see SPASM
  33. MOLEMAN to do all sorts of things with/to PDB files (obsolete except for a few arcane options; use MOLEMAN2 instead !)
  34. MOLEMAN2 to do everything you used to do with MOLEMAN, but: better, stronger, faster !
  35. MSEQPRO to generate PROSITE-formatted profiles from a set of aligned protein sequences
  36. MSEQ2ALSC to convert multiple sequence alignment files from STRUPRO or PRF2MSEQ into input files for ALSCRIPT
  37. NCS6D to find NCS operators
  38. NHANCE: not documented
  39. O2D to make 2D plots
  40. ODBM to analyse O datablocks (ODBMAN offers many more options !)
  41. ODBMAN to analyse O datablocks
  42. ODLEDIT: not documented
  43. OOPS2 to scrutinise your model and generate rebuilding macros for O
  44. OOPS (obsolete; superceded by OOPS2)
  45. OST: not documented (obsolete; superceded by SOD)
  46. PACMAN to check packing after Molecular Replacement
  47. PDB2CT: not documented
  48. POST: obsolete !
  49. PREDIC: not documented or released
  50. PRF2MSEQ to convert the results of a profile/database scan into a partial multiple sequence alignment, suitable as input to MSEQPRO
  51. PRO1: obsolete !
  52. PRO2: obsolete !
  53. PROF to generate electron-density profiles (only in Uppsala at present)
  54. QDB is a program to query a database containing statistics and quality information for 476 X-ray protein structures
  55. RIGOR to find predefined motifs from other structures in your model
  56. RMSPDB to analyse multiple models (LSQMAN does this much better !)
  57. SAVANT to do an all-atom superpositioning of SPASM hits
  58. SEAMAN to generate search models for Molecular Replacement
  59. SEQMAN to read, write and align protein sequences
  60. SITE2RT to find RT-operators between (heavy atom or selenium) sites in different crystal forms
  61. SOD to generate O datablocks from (aligned) sequences
  62. SOLEX to extract the best solutions from ESSENS runs (and to attempt to auto-trace helices and strands)
  63. SPANCSI investigate if your NCS-related molecules have very different average temperature factors, and if so, take special measures during averaging
  64. SPASM to find motifs of main and/or side chains (includes MKSPAZ documentation)
  65. SSENCS to find NCS operators in sets of SSEs
  66. STRUPAT to generate PROSITE patterns from a set of superimposed 3D protein structures
  67. STRUPRO to generate PROSITE-formatted profiles from a set of superimposed 3D protein structures
  68. VOIDOO to find cavities and analyse volumes
  69. XPAND to expand molecules under NCS and/or spacegroup symmetry
  70. 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
  71. XVRML to generate VRML files from PDB files
  72. ZPROF to calculate Z-scores from the results of a profile/database scan

USF Latest update at 26 August, 2008.