Uppsala Software Factory - X-UTIL Package
Download executables (SGI|ALPHA|LINUX|OSX) |
Download databases & libraries |
- AVEPDB to average models
- CELLO to play with your cell
- CT2HET to find hetero compounds in
the PDB using only atom type and connectivity information (using the
hetero-compound collection OMAC/hetero.pdb)
- DCUP to do quick calculations
- HETZE to check the geometrical
quality of hetero compounds (before or after refinement)
- LIGCOM to check and compare
the geometry of hetero compounds
- 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 !
- O2D to make 1D and 2D plots
- ODBM to analyse O datablocks
(ODBMAN offers many more options !)
- ODBMAN to analyse O datablocks
- OOPS2 (OOPS
is obsolete) to scrutinise your model and generate rebuilding macros for O
- PACMAN to check packing after
- RMSPDB to analyse multiple models
(LSQMAN does this much better !)
- SEAMAN to generate search models
for Molecular Replacement
- SOD to generate O datablocks from
- 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
- Not documented yet: OST (superceded by SOD), ODLedit, PDB2CT
Example of a "CONS" CA-trace. Using task MULT and an alignment of
163 fasciculin sequences, SOD produces O datablocks and a macro. CONS
is a CA-trace colour-ramped by the percentage conservation of the residue
type that occurs in the structure compared to the complete set of
sequences. Blue means little conservation, red means a lot.
Example of a "GRAD" CA-trace. See above for details. GRAD is a
CA-trace coloured by the percentage conservation in steps of 20%.
Example of a "VARI" CA-trace. See above for details. VARI is a
CA-trace colour-ramped by the number of different residue types
at each position.
Example of a "ENTR" CA-trace. See above for details. ENTR is a
CA-trace colour-ramped by the entropy at each alignment position.
- Trouble ftp-ing through your browser ?
Look here !
- MOLEMAN2 server to generate Ramachandran,
C-Alpha-Ramachandran, and Duarte-Pyle plots, as well as
an O macro that will do RS-fit, pep-flip and RSC and create datablock files
needed for running OOPS(2)
O macro for quick generation of arbitrarily long alpha-helices (uses MOLEMAN)
O macro for quick generation of arbitrarily long beta-strands (uses MOLEMAN)
script that uses ODBMAN and O2D to produce plots of a pep-flip and
an RSC-fit datablock file (including a scatter plot relating these two
script to generate dictionary files for a hetero compound from
the hetero.pdb collection file
same as het_dicts, but extracts all examples of a hetero compound from structures
solved at 2.0 Å resolution or better
collection of many, many HETERO compounds extracted from the latest
PDB release and all translated to (0,0,0)
MOLEMAN2 macro; almost fool-proof way to apply an AMORE solution
MOLEMAN2 macro; list all sorts of statistics about your B-factors and
make some plots
MOLEMAN2 macro; generates a cute VRML world (file) from any PDB file
MOLEMAN2 macro; go from an X-PLOR model to an O model and run quality
checks and list B-factor statistics and create some useful O macros
(e.g., to run pep-flip etc.) within a minute !
MOLEMAN2 macro; convert O model into PDB files suitable for X-PLOR
*and* auto-generate an X-PLOR GENERATE input file
MOLEMAN2 macro; generates an ODL file with a
least-squares plane for a glucose residue (GLC; can be changed by
editing the file, of course)
MOLEMAN2 macro; check some quality aspects of your protein
MOLEMAN2 macro; convert X-PLOR model into PDB file suitable for O/CCP4
script to extract real-space R-values from CNS into an O-style datablock for use with OOPS(2)
script to produce PostScript plot of Rfree and Rcryst versus
progress of X-PLOR refinement (uses O2D)
script for quick conversion of O2D plot files into PostScript or
- Tutorial: Visualisation of planes. This
explains how to visualise least-squares planes in O. The tutorial
uses only Uppsala programs (MOLEMAN2 and O). In the example, a
chain of nine twisting glucoses inside CBH I is visualised.
X-UTIL (pronounce: "subtle") is a set of utility programs intended for
(but not limited to) practicing protein crystallographers.
X-UTIL is available for SGI, DEC ALPHA, LINUX and OSX systems.
Some of the programs are useful only if you use O or
X-PLOR/CNS, others are of general utility.
- GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International
Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356,
- GJ Kleywegt, J. Mol. Biol., 273,
- GJ Kleywegt & TA Jones, Meth. Enzymol.,
277, 208-230 (1997).
- GJ Kleywegt & TA Jones, Structure, 4,
- GJ Kleywegt & TA Jones, Acta Cryst., D52,
- GJ Kleywegt & TA Jones, Structure, 4,
Latest update at 2 May, 2006.