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Utility Software


This page describes and provides links to miscellaneous utility software developed in our laboratory. All programs are free and open-source. A description for use of each program is available from the "README.program" link, found in the program description and on the download page. These instructions are also included in the "tar" file for each program.

Older versions, experimental versions, and source code are available through our FTP site. Older versions might be desirable either if: a) you are using an old operating system, such as Windows 3.1 or a 68K Macintosh; or b) you find a fatal bug in the current version - if so, please report it. Help is available for using our FTP site, and for trouble shooting downloads in general. If problems persist, please contact us: Feedback.

Items on this page:
> Contouring - 2D and 3D contours, on orthogonal grids
> Dang - dihedral angles from PDB files
> Cluster - groups interacting objects
> PDBCNS - converts between PDB & CNS formats
> Bndlist - finds covalent and hydrogen bonds
> Atvol - molecular van der Waals volume
Software available from two other software pages:
Display Software Page — for Prekin, Mage and JavaMage

All-Atom Contact Programs — for Reduce, Probe and associated scripts

Contouring Programs

3D contours of dot density Kin2Dcont and Kin3Dcont read value/coordinate lists to produce contour maps in kinemage format. Both scattered data and uniformly sampled data can be contoured. Kin2Dcont can also be used to produce contours in PostScript format.

One use of these routines is to contour the average number of contact dots or atomic density for a molecule. Here is a brief description of how to generate contours for contact dots using the script scoreDotsAtAtom, Alternatively, one can contour based on the average atomic volume via this method using the awk script mapvol. Both scripts are available on the scripts download page.


README.kincontours gives further information on use of both Kin2Dcont and Kin3Dcont.

Go to the  KinContour Downloads page to download the current distribution version and documentation.

Go to the  FTP Site  for archived versions and source code.

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Dang

Measuring a dihedral Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formated for easy parsing by awk, grep, sort and other UNIX utilities.


README.dang gives further information on use of Dang.

Go to the  Dang download page  to download the current distribution version and documentation.

Go to the  FTP Site  for archived versions and source code.

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Cluster

Disjoint subsets Cluster is a simple unix C++ program that builds collections of interacting items from records containing interacting pairs or larger fragments. It is part of the algorithm used in Reduce to find H-bond "cliques", and it is called by the clashlistcluster script.


README.cluster gives further information on use of Cluster.

Go to the  Cluster download page  to download the current distribution version and documentation.

Go to the  FTP Site  for archived versions and source code.

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PDBCNS

PDBCNS is an Unix utility that converts between PDB and CNS formats, renumbering H atom names to give the handedness desired by each format and converting between chain ID's and SegID's. It comes in two versions, either a Perl script (recommended) or else a pair of shell and awk scripts. For documentation, read the file header or type the program name with no parameters.


README.pdbcns gives further information on use of pdbcns.

Go to the  scripts download page  to download the current distribution version and documentation.

Go to the  FTP Site  for archived versions and source code.

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Bndlst

Bonded atoms Bndlst reads a PDB format file and for each atom prints a list of covalent and H-bonded neighboring atoms, along with several atomic properties. It is useful in building scripts which process atomic structures.


README.bndlst gives further information on use of Bndlst.

Go to the  Bndlst download page  to download the current distribution version and documentation.

Go to the  FTP Site  for archived versions and source code.

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Atvol

van der Waals spheres This program performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume.


README.atvol gives further information on use of Atvol.

Go to the  Atvol download page  to download compiled binaries for SGI (irix) and Linux.

Go to the  FTP Site  for source code.

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