All-Atom Contact Software

Software available from this page are the tools generated in our laboratory to do all-atom contact analysis of macromolecular models. All-atom contact analysis is more fully explained in the validation section of this site. The two major programs for this technique are Reduce and Probe. Reduce will add and optimize explicit hydrogens to your PDB file. Probe then takes that "reduced" PDB file and determines the placement of contact dots to represent relationships between atoms' van der Waals surfaces. One can visualize these dots and structural model in Mage, O or XtalView and either investigate identified trouble areas (clashes), or appreciate the beauty of a well-done structure.

You can see most of the functionality of Reduce & Probe by running our new web service, MolProbity. The graphical display is handled by JavaMage instead of Mage, plus, you lose the interactive updating of the contact dots during model changes; but, MolProbity will give you a good feel for what is available in the Probe/Reduce--Mage/Prekin system for all-atom analysis. There are three different ways to use this site: 1) For a small model, you can run validation and see the results directly on MolProbity; 2) You can run the validation programs on MolProbity and download the results for viewing; 3) You can use it to try out our tools.

Below you will find capsule descriptions of Reduce, Probe and associated shell scripts. "README-type" documentation files have been converted to HTML and are available as further description of program functionality and use. All programs are free and open source and can be obtained from the linked download pages, or directly from our FTP site. The download pages access current distribution versions; while older or experimental versions and source code are available via the 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.) A description of our FTP site is available, as is help in case you have problems with a file download. If problems persist, please contact us: Feedback.

Items on this page:: Reduce — adds & optimizes hydrogens; Probe — calculates all-atom contacts; Asn/Gln/His flipkin script — helps evaluate optimum side-chain amide and imidazole orientation; Clashlistcluster — organizes clashscores of your model; NA contacts — nucleic acid base stacking and packing; Autobondrot — probe scores on grid of dihedral angle values; Probescripts for O or XtalView — use of all-atom contact analysis while model building
... and please don't forget that there are two other software pages:: Display Software Page — for Prekin, Mage and JavaMage; Utility Software — for miscellaneous executables and scripts

Reduce: Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH₃⁺, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided. A slightly modified version of the connectivity table published by the PDB is included (reduce_het_dict.txt). The program is described in Word, et al.(1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" J. Mol. Biol. 285, 1733-1745.

Version 2 of Reduce is a C⁺⁺ program developed on a Silicon Graphics workstation. It was written by J. Michael Word in the laboratory of David and Jane Richardson, at Duke University.; README.reduce gives further information on use and installation.

Go to the Reduce Downloads page for current distribution versions which contain Reduce, the hetero dictionary, and documentation.

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

Probe: The program Probe allows one to evaluate atomic packing, either within or between molecules. It generates "contact dots" where atoms are in close contact. For a detailed description see Word, et al. (1999). "Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms" J. Mol. Biol. 285, 1709-1731.

Essentially the inverse of the Connolly algorithm, the approach is to place a very small probe (typically of radius 0.25A) at points along the van der Waals surface of a selected set of atoms and determine if this probe also contacts atoms within a second "target" set. Probe provides a flexible method for selecting the source and target atoms along with command line flags for altering the probe radius and dot density. In addition, Probe can generate contact surfaces within a set of atoms ("self dots") and even "surface dots" where there are no nearby atoms. Click here for a 2MB kinemage showing self contact dots for T4 lysozyme.

Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file (O and XtalView graphics formats are also supported). Alternatively, the packing information can be quantified and displayed in a table listing scores for van der Waals interactions, H-bonds and atomic overlaps ("clashes").

Meaningful analysis of molecular contact surfaces requires that ALL atoms are considered. Before using Probe, use the companion program Reduce to add hydrogens to the coordinate file. Some of the sidechain interactions considered by Reduce are illustrated by contact dot kinemages Asn & Gln sidechain flips in peroxidase and interacting Asn-His-His sidechains in cellulase.

Mage can now use Probe to update contact dots when interactively changing dihedral angles. This is useful, for example, when modeling sidechain conformations as described in Word et al. (2000) Protein Sci. 9, 2251-2259.

Beginning with version 2.0, Probe can scan a set of dihedral angles, generating the probe score for each conformation. For more information, see autobondrot.

Probe is a C program developed on a Silicon Graphics workatation. It was written by J. Michael Word in the laboratory of David and Jane Richardson, at Duke University.; README.probe gives further information on use and installation.

Go to the Probe Downloads page for tarfiles which contain current distribution versions of Probe and documentation.

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

Asn/Gln/His Flipkin Script: The Flipkin script starts from your input PDB file and choreographs Reduce, Probe, and Prekin to produce a kinemage that animates between the two orientations for each relevant sidechain. This allows you to evaluate the H-bonding and the atomic clashes in your model which led to the flip orientation selected by Reduce. An example of Flipkin use is given in our validation section.

Flipkin requires Perl to be available on your computer or network. Perl is open source, free, and available. However, if you don't have ready access to Perl, then an older collection of Awk scripts is available in the software/scripts/ directory of our FTP site.; README.flipkins gives further information on use and installation.

Go to the Scripts Downloads page for tarfiles which contain current distribution versions of the flipkin perl script and documentation.

Go to the FTP Site for archived versions.

Clashlistcluster: This unix script, which requires Probe, Awk, and Cluster) finds all atom pairs clashing more than 0.4 Å, and prints out a list of them grouped into local clusters and sorted by the worst clash in each cluster. The pre-compiled binary program, Cluster, is included in the tar file with Clashlistcluster.; README.clashlistcluster gives further information on use and installation.

Go to the Scripts Downloads page for tarfiles which contain current distribution versions of Clashlistcluster, Cluster and documentation.

Go to the FTP Site for archived versions.

NAContacts: A Perl script written by J.M. Word, which uses Probe to calculate a table of base-stacking areas and scores, either between base layers or between single bases. It operates on a nucleic acid PDB file with all H atoms (usually added with Reduce). To visualize the contacts quantified in the output table, look at the kinemage file that NAcontacts produces (or run Probe with "base" as the atom selection). If you have Java enabled, GCstacks will show you an example.; README.nacontacts gives further information on use and installation.

Go to the Scripts Downloads page for the tarfile which contains current distribution version of NAcontacts.

Go to the FTP Site for archived versions.

Autobondrot: Changes in probe scores for ranges of dihedral angle conformations can be explored with the command line flag —autobondrot available in versions of Probe 2 or later. The usefulness of this is as described in Word et al. (2000) Protein Sci. 9, 2251-2259. To run Probe with the —autobondrot flag requires a ".rotscr" input file. An Awk script, mkrotscr, which reformats the &bondrot section of a kinemage file into the ".rotscr" input file is packaged with a tutorial example.; README.autobondrot gives further information on use and installation.

Go to the Scripts Downloads page for tarfile which contains the Autobondrot script, a tutorial and documentation.

Go to the FTP Site for archived versions.

Using Probe within O and XtalView: Contact dots output from Probe can be used with model rebuilding in two popular programs, O and Xtalview. Unix/Linux shell scripts to conduit the dot information between Probe and these two model building programs are available. More information is provided in the validation section of this site, specifically the Crystallography page.; These documents describe how one can use Probe with O or Probe in XtalView.

The O macro and script needed to update contact dots while fitting in O are available on the Scripts Downloads page. The script and macro work in either version 7 or 8 of O.

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