These are the software packages that are currently available on
our systems. After a brief description of each program are the unix
commands
that run the program. The commands are case sensitive.
We will add additional capabilities as necessary.
Our core program, InsightII is used to create, display, and rotate
3-dimentional
chemical structures with built-in support for proteins and nucleic
acids.
The structures can be selectively colored and rendered for aiding
analysis.
Manual (pdf)
Type: insightII
Modules:
Discover3
Minimization methods are explained in the Forcefield-Based Simulations manual (pdf)
A molecular modeling and simulation enviorment with specific docking modules.
Type:c2
MODELLER models protein 3D structure by satisfaction of spatial
restraints.
In principle, the restraints can be derived from a number of different
sources. These include homologous structures (comparative modeling),
NMR
experiments (NMR refinement), rules of secondary structure packing
(combinatorial
modeling), cross-linking experiments, fluorescence spectroscopy, image
reconstruction in electron microscopy, site-directed mutagenesis,
intuition,
residue-residue and atom-atom potentials of mean force, etc. The output
of MODELLER is a 3D structure of a protein that satisfies these
restraints
as well as possible. The optimization is carried out by the variable
target
function procedure employing methods of conjugate gradients and
molecular
dynamics with simulated annealing. MODELLER can also do several other
tasks,
including multiple comparison of protein sequences and/or structures,
clustering,
and searching of sequence databases.
MODELLER manual
You must have all the pdb files in the same directory that you will run or a link to them in a pdb database. They must be named the same as the corresponding line in the alignment file.
Version 8v2 is the most recent public release (02/06)
Type: mod8v2 filename.top
To run the tutorial or get a default top file
Type: cp /usr/share/bin/tutorial-model.tar ./ (there is
Type: tar -xvf tutorial-model.tar
Type: cd tutorial-model
Edit model-default.top as necessary
Type: mod8v2 model-default.top
A group of protein and DNA sequence analysis. progams including:
Comparison ,Database Searching and Retrieval ,DNA/RNA Secondary
Structure
,Evolution ,Fragment Assembly ,Gene Finding and Pattern Recognition
,Primer
Selection ,Protein Analysis ,Translation
The programs can be run with a command line or graphics interface.
For command line:
Telnet to beatrice.rutgers.edu
Type:source /usr/local/gcg/gcgstartup
Type:gcg
Type:gcgsupport
You can begin to use the gcg command line as usual.
For graphic interface:
Connect to beatrice.rutgers.edu using a X windows emulator
Type:source /usr/local/gcg/gcgstartup
Type:gcg
Type:gcgsupport
Type: seqlab
This program gathers function information from gene chip experiment data.
Sample input file: filename.csv
Sample outputfile: filename.out.csv
Type:chipgather
Enter:[filename.csv]
Enter:[Starting Point- usually 1]
(If the program is interrupted it canbe restarted at the point of
interruption)
The program requires a very specific input format(see sample input
file).
The data must start on the second line. There must be 7 columns
of data. The second column must contain the accession number in
form
XX:XXX and the experiment values must be in the seventh column.
The program can be modified if a different format is required.
This program takes the output from the chipgather program and counts
the number of genes for each function.
Sample outputfile: filename.out.sort.csv
Type:chipsort
Enter:[filename.out.csv]
The data obtained with the chipgather program is now supplied by
some genechip companies, so the sorting program has been modified to
accept function data from these files. The output now
contains the common name for the gene and the ratio value from the
experiment.
Sample input file:filename2.csv
Sample output file:filename2.sort.csv
Type:chipsort2
Enter:[filename.csv]
This program gathers the Gene Size, CDS region, and sequence from a
list of accession numbers.
Sample output file:filename3.nuc
Type:mrnagather
Enter:[Starting Point- usually 1]
(If the program is interrupted it can be restarted at the point of
interruption)
This program uses the output from the Mrnagather program to search
for patterns in the 5',CDS,and 3' regions. The program accepts
wildcards x, y(a or g), and z (c or t) and can be set to match any
percentage of the pattern.
Sample output file:filename3.nuc.mat
Type:mrnasearch
Enter:[filename3.nuc]
Enter:[output extension] (recommend adding a number to the end for
mulitple searches)
Enter:[filename.seq] (name of file containing the sequence pattern to
match
Enter:[Y/N] (to include or exclude CDS region)
Enter:[1-100] (percent of pattern to match
note:patterns with multiple wildcards and low percent match will yield
a large number of hits)
A suite of automated docking tools. It is designed to predict how
small
molecules, such as substrates or drug candidates, bind to a receptor of
known 3D structure.
Manual
Type:autodock
For the graphical interface:
Type:autodockgr
Type: volume
Calculates the accessibility of the van der Waals surface of atoms
to
a probe sphere of a given radius specified by the user.
The file should not contain hydrogens.
Type: access
Enter an output file name (extension .acc is our convention)
Enter 1 for the number of coordinate files.
Enter an input file name
For format type: BNL
Check the default format to see if it matches your file format
To accept defaults type each of these followed by a return:
NEXT (The number of atoms assigned default radii should be very low,
if it is not, check the format or the hydrogens. You can
use
the h.strip or reduce programs to remove hydrogens.)
NEXT
ALLATM
NEXT
NEXT
Note: Requires a file with no hydrogens
Takes an output file from the access program and distributes the amino acids into groups based on electrostatic properties.
Type: bins
Enter an input file name (usually *.acc)
Enter an output file name
Removes hydrogens from PDB formatted files.
Type:H.strip <pdb input file> <output file>
Intended for shading multiple aligned sequence files.
Manual
For small data sets try the BOXSHADE
Server.
For large data sets:
Copy six files to the directory from which you will run the program.
Type:cp /usr/share/bin/boxshade3.3.1/box_pep.grp ./
Type:cp /usr/share/bin/boxshade3.3.1/box_pep.par ./
Type:cp /usr/share/bin/boxshade3.3.1/box_pep.sim ./
Type:cp /usr/share/bin/boxshade3.3.1/box_dna.grp ./
Type:cp /usr/share/bin/boxshade3.3.1/box_dna.par ./
Type:cp /usr/share/bin/boxshade3.3.1/box_dna.sim ./
This only needs to be done the first time you run boxshade.
Type:boxshade
Answer the questions. For most questions the default values are
fine, however you must type in the input file name, and the output file
name, and the file type must match the input file.
It is recommended also that the question "should position numbers be
printed?" be answered "y" instead of the default no. This
will
yield a more useful printout.
A program for creating schematic or detailed molecular graphics
images
from molecular 3D coordinates
Manual
Type:molscript
Extensions to the program molscript
Manual
Type:bobscript
MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
Telnet to beatrice.rutgers.edu
Type: molmol
VMD is designed for the visualization and analysis of biological
systems
such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may
be used to view more general molecules, as VMD can read standard
Protein
Data Bank (PDB) files and display the contained structure. VMD provides
a wide variety of methods for rendering and coloring a molecule: simple
points and lines, CPK spheres and cylinders, licorice bonds, backbone
tubes
and ribbons, cartoon drawings, and others. VMD can be used to animate
and
analyze the trajectory of a molecular dynamics (MD) simulation. In
particular,
VMD can act as a graphical front end for an external MD program by
displaying
and animating a molecule undergoing simulation on a remote computer.
Manual
Telnet to beatrice.rutgers.edu
Type: vmd
Software for looking at macromolecular structure and its relation to
function
Manual
Telnet to beatrice.rutgers.edu
Type: rasmol
A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared in order to better communicate ideas that depend on 3-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations.
Type: prekin
Type: reduce "filename"
(use -Help for detailed usage description)
Type: probe "inputfile.pdb" >> "outputfile.kin"
(use -Help for detailed usage description)
Desktop energy minimization and molcular visualization software.
This program cannot be run over the network.
Log onto beatrice.rutgers.edu
Type: sculpt
Raster3D is a set of tools for generating high quality raster images
of proteins or other molecules. Ancillary programs process atomic
coordinates
from Brookhaven PDB files into rendering descriptions for pictures
composed
of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can
also
be used to render pictures composed in Per Kraulis' program MOLSCRIPT
in
glorious 3D with highlights, shadowing, etc. Output is to pixel image
files
with 24 bits of color information per pixel.
Raster3d manual
by arrangement
Phylogenetic Analysis Using Parsimony (PAUP) software package for
inference
of evolutionary trees.
PAUP4 manual (pdf)
by arrangement