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.
- ACONIO to split PDB files with
alternative conformations so they can be used in O
- ALPHABET: not documented or released
- AVE for single-crystal averaging
- AVEPDB to average models
- CELLO to play with your cell
- COMA to find NCS mask using
local correlation maps
- COMAP to combine maps during
multiple-crystal averaging
- COMDEM to combine multiple
domain maps
- CRAVE to auto-generate a C-shell
script to do N cycles of averaging over M crystal forms, each
with or without NCS
- CT2HET to find hetero compounds in
the PDB using only atom type and connectivity information (using the
hetero-compound collection OMAC/hetero.pdb)
- DATAMAN to manipulate reflection datasets
- DCUP to do quick calculations
during data-collection
- DEJANA: see DEJAVU
- DEJAVU to find motifs and to
recognise other proteins with a similar fold (includes
documentation for DEJANA, PRO1, PRO2 and POST)
- ESSENS to do real-space searches
for fragments (e.g., helices) or molecules
- FITAL: not documented or released
- FLOOD to fill a cavity with water
molecules
- HETZE to check the geometrical
quality of hetero compounds (before or after refinement)
- IMP to improve NCS operators
- LSQMAN to superimpose and analyse
multiple models and/or molecules
- MAKRIG: see RIGOR
- MAMA to manipulate masks
- MAPFIX add spacegroup and symmetry
operators to a CCP4 map
- MAPMAN to manipulate maps
- MAPPAGE: not documented (obsolete; use MAPMAN instead)
- MAPROP to produce maps of various
properties
- MASKIT to find cross-crystal averaging
mask using local correlation maps
- MAVE for multiple-crystal averaging
- MKSPAZ: see SPASM
- MOLEMAN to do all sorts of
things with/to PDB files (obsolete except for a few arcane
options; use MOLEMAN2 instead !)
- MOLEMAN2 to do everything you
used to do with MOLEMAN, but: better, stronger, faster !
- MSEQPRO to generate PROSITE-formatted
profiles from a set of aligned protein sequences
- MSEQ2ALSC to convert multiple
sequence alignment files from STRUPRO or PRF2MSEQ into input
files for ALSCRIPT
- NCS6D to find NCS operators
- NHANCE: not documented
- O2D to make 2D plots
- ODBM to analyse O datablocks
(ODBMAN offers many more options !)
- ODBMAN to analyse O datablocks
- ODLEDIT: not documented
- OOPS to scrutinise your model and
generate rebuilding macros for O
- OST: not documented (superceded by SOD)
- PACMAN to check packing after
Molecular Replacement
- PDB2CT: not documented
- POST: see DEJAVU
- PREDIC: not documented or released
- PRF2MSEQ to convert the results
of a profile/database scan into a partial multiple sequence
alignment, suitable as input to MSEQPRO
- PRO1: see DEJAVU
- PRO2: see DEJAVU
- PROF to generate electron-density profiles
(only in Uppsala at present)
- QDB is a program to query a database
containing statistics and quality information for 476 X-ray protein
structures
- RIGOR to find predefined motifs
from other structures in your model
- RMSPDB to analyse multiple models
(LSQMAN does this much better !)
- SEAMAN to generate search models
for Molecular Replacement
- SITE2RT to find RT-operators between
(heavy atom or selenium) sites in different crystal forms
- SOD to generate O datablocks from
(aligned) sequences
- SOLEX to extract the best solutions from
ESSENS runs (and to attempt to auto-trace helices and strands)
- SPANCSI investigate if your NCS-related
molecules have very different average temperature factors, and if so,
take special measures during averaging
- SPASM to find motifs of main and/or
side chains (includes MKSPAZ documentation)
- STRUPAT to generate PROSITE
patterns from a set of superimposed 3D protein structures
- STRUPRO to generate PROSITE-formatted
profiles from a set of superimposed 3D protein structures
- VOIDOO to find cavities and analyse
volumes
- XPAND to expand molecules under
NCS and/or spacegroup symmetry
- 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
- XVRML to generate VRML files from PDB files
- ZPROF to calculate Z-scores
from the results of a profile/database scan
Latest update at 14 September, 1998.