Uppsala Software Factory - Inverted index

All program documentation is © G.J. Kleywegt, 1992-1998.

Contents:

• Protein purification
• Crystallisation
• Data-collection
• Data-analysis and manipulation
• Direct methods
• Patterson interpretation
• Building in a MIR(AS)/MAD map
• Molecular Replacement
• Density modification
• Map manipulation
• Quality control
• Model rebuilding
• Refinement
• Model analysis
• PDB deposition
• Miscellaneous

• DCUP helps you with lots of quick calculations that you typically need to do during data-collection (cell volume, Vm, missetting angles, data-collection time, crystal to detector distance, etc.)

• DATAMAN
  1. format conversion
  2. apply conditions of Laue group
  3. list or delete certain reflections (rogues, resolution, etc.)
  4. statistics, histograms and plots
  5. compare, scale and combine pairs of datasets
  6. Wilson scaling of two datasets
  7. sort and re-index
  8. anisotropy analysis
  9. twinning analysis
  10. guesstimate completeness, Vm, effective resolution etc.
  11. design a proper refinement protocol
  12. modify Fs and sigmas
  13. list special reflections or systematic absences
  14. calculate Rsym of hkl and khl reflections
  15. calculate internal Rmerge in any Laue group

• DATAMAN to generate delta-F files for use with SHELXS

• MAPMAN to contour Harker sections
• MOLEMAN2 to convert coordinates between fractional and Cartesian space

• MAPMAN to mappage and skeletonise density
• DEJAVU to compare secondary structure elements identified in the skeleton to the database of known protein structures to look for fold similarities
• ESSENS to look for helices, strands or other entities; SOLEX to extract the best solution(s) (and to attempt to auto-trace helices and strands); DEJAVU to look for known protein structures with a similar fold
• SOD to generate an O datablock with the sequence of your protein
• MOLEMAN to generate bits of ideal helix and strand to plug right into your structure

• DATAMAN to generate X-PLOR reflection files
• XPLO2D
  1. convert certain X-PLOR output files into O2D plot files
  2. analyse PC-refinement or direct rotation function output and produce rotman or PC-refinement input files
• MAPMAN to convert X-PLOR 3dmatrix files to O or other type maps
• PACMAN to check possible AMORE solutions
• SOD to generate a search model in the case of reasonably high sequence homology
• SEAMAN to generate search models quickly (lots of useful options; suitable for multiple models)
• LSQMAN to superimpose several models (e.g., NMR or NCS) to get a multiple search model
• MOLEMAN2
  1. convert a model to CA-only, poly-Gly, poly-Ala, or poly-Ser
  2. change temperature factors and occupancies
  3. apply (AMoRe) solutions to a search model
  4. calculate radius of gyration
  5. show distribution of intra-molecular distances to find a reasonable Patterson integration radius
  6. align inertia axes with X, Y and Z (as in AMoRe's TABLING step)
• ESSENS to do 6D real-space searches in cases where phase information is available (MIR(AS), MAD, or a partial Molecular Replacement solution); SOLEX to extract the best solution(s)

• MAMA to generate, manipulate, combine, improve and analyse masks (molecular envelopes)
• NCS6D to find NCS operators
• COMA to find NCS masks using local NCS correlation maps
• IMP to improve NCS operators
• AVE for single-crystal averaging, or SPANCSI if your molecules have very different average temperature factors
• DATAMAN to apply Wilson scaling to multiple datasets for multiple-crystal averaging
• CRAVE to auto-generate a C-shell script to do N cycles of averaging over M crystal forms, each with or without NCS
• MASKIT to find cross-crystal averaging mask using local correlation maps
• MAVE for multiple-crystal averaging and inter-crystal operator improvement
• COMAP to combine maps during multiple-crystal averaging
• COMDEM to combine multiple domain maps
• MAPMAN to apply digital image filtering techniques to maps (untested as a density-modification tool)
• SITE2RT to find RT-operators between (heavy atom or selenium) sites in different crystal forms

• MAPMAN
  1. format conversion (CCP4, X-PLOR, EZD, DSN6, BRIX, ...)
  2. MAPPAGE functionality to produce O-style (DSN6 or BRIX) maps
  3. analyse, normalise, scale, add to and multiply maps
  4. compare and combine pairs of maps
  5. skeletonisation (BONES)
  6. swap bytes on old VAX-DSN6 files
  7. peak-picking
  8. extract 2D planes for contouring with O2D
  9. 1D and 2D projections
  10. map cosmetics ("filters")
  11. cut & paste from one map to another
  12. integrate and zero parts of a map
• MAPFIX add spacegroup and symmetry operators to a CCP4 map
• MAVE EZ skewing of a map !!!

• MOLEMAN2
  1. Ramachandran plots and main-chain quality
  2. RMS delta-B bonded and non-bonded atoms
  3. quality assessment of CA-only models
  4. temperature-factor plots (average, RMS, radial)
  5. nomenclature and quality of side chains
  6. short contacts
• LSQMAN analyse differences between NCS-related molecules (or shifts during refinement) in terms of position, dihedrals, CA-geometry, waters and temperature factors
• ODBMAN create O/OOPS datablocks from X-PLOR, PROCHECK or other output files
• OOPS
  1. various quality checks, statistics and plots
  2. comparison with previous model
  3. automatic generation of rebuilding macros for O
• O2D analyse plot files from MOLEMAN, OOPS, etc., and convert to PostScript or CricketGraph format
• XPAND to list and classify close (NCS+SGS) contacts

• OOPS to generate rebuilding macros for O for either all residues, or only those that (may) have problems
• MAPMAN to pick peaks (e.g., potential water molecules)
• MOLEMAN sort water molecules such that Water_add in O will be efficient
• MOLEMAN2
  1. automatic generation of several types of O dictionary files, e.g. for ligands
  2. automatic generation of an O macro to fit all water molecules using the RSR_Rigid command in O
  3. automatic generation of an O macro to run all the checks needed for OOPS
  4. invert coordinates, e.g. of a chiral ligand to get the other enantiomer
• XPAND to analyse if some waters could perhaps be something else
• ACONIO to split PDB files with alternative conformations so they can be used in O

• DATAMAN
  1. generate X-PLOR reflection file
  2. assign Rfree TEST flags in myriad ways
  3. design a proper refinement protocol
  4. prepare data for difference refinement
• CELLO to exchange NCS operators between O and X-PLOR
• CT2HET to find hetero compounds in the PDB using only atom type and connectivity information (using the hetero-compound collection OMAC/hetero.pdb)
• XPAND to generate an X-PLOR include file with an as complete as possible specification of non-crystallographic and crystallographic symmetry (NCS, XNCS) in the case of strict NCS constraints
• XPLO2D
  1. list bad contacts during X-PLOR refinement
  2. automatic generation of X-PLOR dictionaries for hetero-entities (topology, parameter, energy minimisation)
  3. set up harmonic restraints in terms of dihedrals (PHI, PSI, CHI1 and/or CHI2)
• HETZE to check a hetero compound's geometry prior to or after refinement
• MOLEMAN2
  1. add X-PLOR segment IDs to a PDB file
  2. suggest sensible coordinates for X-PLOR OT1 and OT2 atoms
  3. reset, limit, smooth or average temperature factors and occupancies
  4. remove or rename hydrogen atoms
  5. split PDB files to get one file per X-PLOR segment, plus a generate.inp input file for X-PLOR including disulfide patches
  6. geometry analysis of multiple copies of a certain residue type (useful in combination with XPLO2D for writing dictionaries)

• SOD to generate O datablocks and macros based on a comparison of pairs or multiple (aligned) sequences
• DEJAVU to compare your protein to the database, or to identify proteins with similar secondary-structure motifs (analyse the results with LSQMAN, DEJANA and O)
• SPASM to find motifs of main and/or side chains
• RIGOR to find predefined motifs from other structures in your protein
• XPAND
  1. to expand molecules under NCS and/or spacegroup symmetry
  2. list and classify close (NCS+SGS) contacts
  3. analyse if some waters could be something else
• LSQMAN
  1. superpositioning of molecules/models and lots-a-plots (explicit and automatic alignment as well as improvement)
  2. analyse differences between NCS-related molecules or multiple NMR models
• RMSPDB to calculate and plot RMS distances between corresponding atoms in two similar, aligned structures
• VOIDOO to investigate cavities and columes
• FLOOD to closely pack hypothetical water molecules inside a cavity
• MAMA to investigate the tunnels etc. that VOIDOO can't find (a la Delaney)
• MAPROP
  1. produce maps of various properties
  2. visualise cavities etc. a la Voorintholt et al.
• XPLO2D to convert X-PLOR Luzzati output into O2D plot files
• O2D analyse plot files from various other programs, and convert to PostScript or CricketGraph format
• HETZE to check a hetero compound's geometry

• XPAND to generate MTRIX records from O-style NCS-operator files
• MOLEMAN generate various types of REMARK records containing model (quality) statistics
• MOLEMAN2
  1. add CRYST, SCALE and ORIGX cards
  2. generate SSBOND cards
  3. automatically assign atoms to be ATOM or HETATM
  4. generation of chain and segment IDs
  5. add/remove REMARK records
  6. rename atoms and residues (e.g., X-PLOR waters to PDB waters)
• OOPS to generate various types of REMARK records containing model (quality) statistics
• DATAMAN to prepare reflection files in any of a variety of formats

• AVEPDB to average models
• ODBMAN to analyse, compare, manipulate, generate and plot O datablocks
• XVRML to generate VRML files from PDB files
• QDB to query a database containing statistics and quality information for 476 X-ray protein structures (e.g., to see how favourably your structure compares to those)
• MOLEMAN
  1. generate ideal alpha-helices and beta-strands
  2. count residues and chemical elements
  3. estimate molar extinction coefficient at 280 nm
  4. generate an O datablock to colour your molecule in the colours of the Dutch or Swedish flag
• MOLEMAN2
  1. convert Cartesian to/from internal to/from fractional coordinates
  2. add or edit a CRYST1 card
  3. temperature-factor statistics
  4. find potential N-glycosylation sites in your sequence
  5. generate SSBOND records
  6. generate PIR sequence file
  7. generate an ODL file to draw disulfides in O
  8. distance plots
  9. rename atoms
  10. rename and renumber residues
  11. invert or mirror coordinates
  12. random perturbation or rotation of coordinates
  13. locate sequence motifs
• SBIN suite of programs for sequence pattern and profile analysis (using SwissProt and the pftools package)
  1. STRUPRO to generate PROSITE-formatted profiles from a set of superimposed 3D protein structures
  2. ZPROF to calculate Z-scores from the results of a profile/database scan
  3. PRF2MSEQ to convert the results of a profile/database scan into a partial multiple sequence alignment, suitable as input to MSEQPRO
  4. MSEQPRO to generate PROSITE-formatted profiles from a set of aligned protein sequences
  5. STRUPAT to generate PROSITE patterns from a set of superimposed 3D protein structures
  6. MSEQ2ALSC to convert multiple sequence alignment files from STRUPRO or PRF2MSEQ into input files for ALSCRIPT.