Scientific Software (Obsolete) in the MGCF

The MGCF workstations (175 Tan Hall) and Panther computing cluster have a wide variety of software.

The apps on this page are no longer supported but we have remnant copies and exist here as a record. If you want and of these, please dsicuss with us. We can suggest alternatives or revive these as needed.

The notes below refer to software as available on 1) MGCF workstations or 2) Panther (the computing cluster), but these are obsolete so are not being tested or guaranteed to work.

Art of Illusion

is an open source 3D modelling and rendering studio. It can create high quality, photorealistic images and animations. For information and tutorials, see the home page.
AOI is installed on the MGCF workstations (not Panther). Type aoi to start.

Bioinformatics tools

We have an ever growing and changing set of Bioinformatics tools. These include
Bedtools 2.26.0
Bioclipse
FastQC
Trim Galore!
FLASH
SAM Tools
CD-Hit: for clustering DNA/protein sequence data.
Type: bio_setup to activate these programs. Activation is for that shell only.

Dia

Dia is used to create diagrams such as entity relationship diagrams, UML diagrams, flowcharts, network diagrams, and simple circuits. One can add new shapes by writing simple XML files, using a subset of SVG to draw the shape. It can load and save diagrams in XML and other formats.

Type dia to start.

Dock

Dock is as suite of programs to find favorable orientations of a ligand in a receptor. It is a command line driven program and output can be visualized in chimera. Users should read the manual and work the tutorials at the DOCK home page.

You will need to add the executables to your PATH before running.

Gabedit

Gabedit is a graphical interface to chemistry packages such as Gamess, Gaussian, Molcas, Molpro, MPQC and Q-Chem. It is available from from Sourceforge. Note that we recommend IQmol as an interface for Q-Chem.

Type gabedit to start.

Gimp

Gimp is the GNU Image Manipulation Program. It has many features found in Photoshop. This is on the MGCF workstations in 175 Tan Hall (not Panther). Type gimp to start. See the GIMP home page for documentation.

GSAS

GSAS (General Structure Analysis System) is a comprehensive system for the refinement of structural models for x-ray and neutron diffraction data. It can be used with single-crystal and powder diffraction data (Rietveld analysis).

The manual is in the /usr/software/gsas folder. Type gsasgui to start.

GSAS is no longer available but GSAS-II can be obtained from the Argonne National Lab.

We also have NCNR Ciftools which includes pdCIFplot, used to plot of Rietveld results from pdCIF files, and cifedit, used to create and edit CIF files.

Gulp

GULP performs simulations on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). It uses analytical solutions with lattice dynamics, rather than molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons.

To load the environment variables on the workstations, type:
intel
source /home/mgcf/software-ws/gulp-5.2/MGCF_setup-mpi-run.sh
These should be typed once per terminal when you plan to use gulp.

For a multicore job, type:
mpirun -np 2 gulp < example1.gin > example1.gout
For a one core job, type:
gulp example1
Note the lack of file extension or redirect to an output file for the 1 core job.
This 1 core vs multicore syntax is different from what the manual says! The input file is example1.gin in both 1 core and multicore cases, but you only type the example1 prefix in the command to run the 1 core job. In the multicore job, you type the whole file name.

Documentation and example files are in
/home/mgcf/software-ws/gulp-5.2
For more information, see the home page.

Hex

Hex is older program for protein-protein or protein-DNA docking.
Maestro and its related programs are more current for this kind of calculation but we keep Hex in case it is useful for someone.
Hex has built in documentation and tutorials. Type hex to start.
For more information: home page and email us to request our Hex usage notes.

ImageJ

ImageJ is a public domain Java image processing and analysis program to display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and raw. It supports stacks and hyperstacks, a series of images that share a single window.

It can calculate area and pixel value statistics, measure distances and angles, create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

It is installed on the MGCF workstations. Type imagej to start the interactive program. There is suite of command line tools as well.

MMTSB

Multiscale Modeling Tools for Structural Biology. These are tools for dealing with biomolecular structures and related computational data.

See the home page for command documentation.

You will have to type "mmtsb" once per shell session. That will load the MMTSB tools into the shell session and disable similarily named software.

Modeller 9v5

Modeller is used for homology modeling of protein 3D structures. Provide an alignment of a sequence to be modeled with known related structures and MODELLER calculates a model. MODELLER can perform de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. See the home page for tutorials and faqs.

Platon

Platon is a versatile, SHELX97 compatible, multipurpose crystallographic tool. See the home page

Type platon to start the program.

RCSB-LigandExplorer

RCSB-LigandExplorer visualizes Protein Data Bank (PDB) data such as the interactions of bound ligands in protein and nucleic acids structures.
It should auto load in your browser if viewing the PDB site. If not, type ligand_explorer to start the program.

Scilab

Scilab is a free scientific software package for numerical computations in engineering and scientific applications. It includes hundreds of mathematical functions with the a program interface (C, Fortran...). It has sophisticated data structures (including lists, polynomials, rational functions, linear systems...), an interpreter and a high level programming language. Scilab is an open system where users can define new data types and operations.

This is on the MGCF workstations (not Panther). Type scilab_setup to add this to your PATH for the current terminal.
Then scilab will start the GUI. See also scilab-cli scilab-adv-cli for different clommand line interpreters.
More information and documentation is available at the Scilab home page.

Tinker

Tinker is a package for molecular mechanics and dynamics, with special features for biopolymers devleped by the Ponder group at Washington University (St. Louis). It can use Amber, CHARMM, MM2 and MM3, OPLS, MMFF, Liam Dang's polarizable potentials, and the Ponder group's own AMOEBA polarizable atomic multipole force field.

To use the tinker subprograms on the MGCF workstations, type tinker_setup first to set the right environment variables for that shell. See also the folders /home/mgcf/software-ws/tinker/examples and /home/mgcf/software-ws/tinker/params.

Links: home page, There is a GUI called Force Field Explorer.

Tonto

Tonto is a tool for quantum crystallography and quantum chemistry. It can do wavefunction fitting in which Hartree Fock/DFT calculations are constrained by some experimental data, typically from X-ray diffraction studies. It can refine crystal structures using ab initio wavefunctions. It can also fit electronic wavefunctions to X-ray diffraction data.

See also the folders:
/home/mgcf/software-ws/tonto/tests
/home/mgcf/software-ws/tonto/basis_sets

Links: home page, How-to-run page, theory, more theory

Voidoo

Voidoo is older software which detects cavities in macromolecular structures. It is written by Gerard J. Kleywegt at the Uppsala Software Factory.

Voidoo output can be viewed with O or Chimera. Chimera is easier to use but requires conversion of the output data from Voidoo. Use Voidoo to write NewEZD output files. Then use the ccp4 program xdlmapman to convert NewEZD output to CCP4 format. CCP4 format files can be visualized with Chimera's Volume Viewer. We can no longer find links for this.

We also have RAVE from the Uppsala Software Factory. This includes mapman which can convert NewEZD to CCP4 format. Programs and sample files are in /home/mgcf/software-ws/rave.

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