Software and Scripts
Click on the program name to go to the software's website for
instructions and other information
"For improvement and objective interpretation of
crystallographic electron density maps and automatic
construction and refinement of macromolecular models".
Accessable through the CCP4 interface.
"A collection of disparate programs covering most of the
computations required for macromolecular crystallography".
"cns < input.inp > output.out &"
Our lab's most used program for refinement of models. "A
flexible multi-level hierachical approach for the most commonly
used algorithms in macromolecular structure determination.
including heavy atom searching, experimental phasing (including
MAD and MIR), density modification, crystallographic refinement
with maximum likelihood targets".
commands: "xdisp", "denzo", "scalepack", etc..
A program package for the visualization of X-ray diffraction
images ("xdisp"), for data reduction and integration ("denzo"),
and for merging and scaling of the intensities obtained by Denzo
("scalepack"). "denzo" and "scalepack" are command line
executable. For fully integrated graphical interface, see
A holographic method for solving electron density in real-space.
command: "epmr cell.cel model.pdb data.hkl >
An easy to use and relatively fast program for solving
cyrstallographic molecular replacement (MR) solutions using an
evolutionary search algorithm. To generate the EPMR-required hkl
file, run "mtz2vaious" from CCP4 using the "USER" Fortran format
of '(3i4,2F8.2)' and then add two column labels for "FP" and "SIGFP".
A graphical version of Denzo/Scalepack. Several new subprograms
are incorporated, including strategy and simulation, 3-D
processing, mosaicity refinement during processing, variable
spot size, easy change of the space group, report generation,
A submodule of the future PHENIX cystallographic program
package. HySS is "a highly-automated procedure for the location
of anomalous scatterers in macromolecular structures". Note:
"currently the command line interface is limited to work with
anomalous diffraction data" only.
A program for displaying molecular 3D structures in both
schematic and detailed representations. Molscript along with
"Raster3D" can be used to generate high resolution images of 3D
structures in common image formats such as jpg, tiff, and gif.
An alternative for Denzo/HKL. It is a graphical interface of
Mosflm for indexing and integration of X-ray diffraction images.
Create a new directory to run DPS as a lot of temporary files
will be copied and created.
command: "phaser < input.inp > output.out &"
A new alpha (pre-beta) version program for MR, using the maximum
likelihood methods for phasing macromolecular crystal
A new open-source program for molecular modeling. An alternative
commands: "render", etc..
A set of tools for generating high quality raster images of
proteins or other molecules. Raster3D can also be used to render
pictures composed in other programs such as "Molscript" in
glorious 3D with highlights, shadowing, etc.
SnB provides a graphical user interface for computing normalized
structure-factor magnitudes, solving phases by the main SnB
dual-space direct-methods, visualising and editing molecular
structures. The SnB algorithm was entitled "The Top Ten
Algorithms of the 20th Century" in a poster published by
Computing in Science and Engineering in November, 1999.
command: "sharp", or goto
http://localhost:8080/ in web browser.
A program using web
browser interface for solving phases from MIR(AS), SIR(AS), SAD,
and MAD data, as well as for density modification of electron
commands: "shelxc", "shelxd", "shelxe", "shelxh",
"shelxl", "shelxpro", "shelxs", "shelxwat"
"A set of programs for crystal structure determination from
single-crystal diffraction data". shelxc--preparations of files
for phasing; shelxd--structure solution for difficult problems
and location of heavy atoms; shelxe--phases from shelxd heavy
atom stides and density modification; shelxl--structure
refinement (use shelxh for large structure); shexlpro--protein
interface to shelx; shelxs--structure soltuion by Patterson and
direct methods; shelxwat--automatic water divining for
macromolecules. XPREP can be used for preparation of SHELX input
commands: "solve", "solve-huge", "resolve", "resolve_huge"
SOLVE--Automated crystallographic structure solution for MIR,
SAD, and MAD
RESOLVE--Statistical density modification, local pattern
matching, automated model-building, and price-and-switch minimum
A general purpose molecular modelling environment for model
building, viewing of 3D structures, as well as ligand fitting
and protein stacking.
Xprep 6.15 (demo)
commands: "xprep", "bigxprep"
A standalone utility for processing MAD, SIR, SIRAS data;
displaying reciprocal space to check completeness of data;
displaying Harker sections of Patterson maps; and displaying
self-rotation functions to search for non crystallographic
symmetry and twinning.
commands: "xfit", "xtalmgr"
Xfit is our lab most used program for fitting electron density
maps and model building. Xtalmgr, the main menu of XtalView, can
be used for creating new "crystal info" files for Xfit, as well
as for solving structures by MIR and MAD.
command: "cleanpdb.com < input.pdb >
Clean PDB files to retain only the lines of "ATOM" and "HETATOM".
Also remove any character within the empty fields of PDB that is
generated from programs like SwissPDB.
command: "cns2fsfour_linux" or
"cns2fsfour_sgi" then "cns_input.map xfit_output.map"
Directly converts a CNS generated Map file into Xfit readable
Map file. **NOTES: 1) Use the scripts for their corresponding
computer platforms,ie. either Linux or SGI. 2) When generating
the CNS map, look for the "extend of map" option and select
"UNIT". 3) Recommend to creat the Xfit map and actually run Xfit
from the same computer OS-platform or the map may not be read
correctly. 4) To load the newly generate map from the script,
RIGHT click on the "Load Map" tab in Xfit and pull down to
select "Load FSFOUR Map".
command: "cns2xfit.awk cns_input.coeff >
This script convert CNS map coefficent file (.coeff) to Xfit
phase file (.phs).