Home-Page Site-Map

The larger, more complex scripts which we've written are available for download below. A description of what the script does is given. To the right of the description, you'll find: system requirements for script interpretation, the download link, and documentation on script use.

System Requirements

R

Zip File to Download

Documentation

  • README file inside of Zip container

R Script for VTF percentile plot

An R script and R data object are provided for the ClashScore quality parameter as an example of the percentile plots presented by the X-Ray Validation Task Force in its recommendation to the wwPDB.


System Requirements

*awk + Probe + Cluster

Download link

Documentation

ClashList

The ClashList shell script uses Cluster, Probe and awk to group and sort clashes by interacting residues. Besides providing a list of clashes grouped by residue and sorted worst first, the script calculates summary statistics for the molecule. Probe and Cluster can be downloaded from the links provided above and at right.


System Requirements

Download links

Documentation

  • README file for perl version
  • README file for awk version

Flipkin

Flipkin works with Reduce, Probe and Prekin to help you decide the best "flip state" for asparagine, glutamine, and histidine. Flipkin will generate recommendations as to correct orientation, 'flip', of the sidechains of Asn, Gln and His. It will also generate kinemages of the flips and with all-atom contact dots for your selection of the best flip state. The newer version of this script uses perl; an older version using awk rather than perl is also available at right


NAContacts

NAContacts is a perl script 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).


System Requirements

Download link

Documentation

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 {download arrow PDF, 188KB}. 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.


System Requirements

Download link

Documentation

ScoreDotsAtAtom

Bookkeeping of all-atom contact dots by each atom. Typically used to generate raw data for kincontours.


System Requirements

Download link

Documentation

MapVol

awk script to assign volume by atom.


System Requirements

  • perl or awk
  • Kin3Dcont
  • Probe
  • BndLst

Download link

Documentation

PDBCNS

PDBCNS interconverts atom names between the PDB and CNS formats. It is available as an older version using awk or a newer version using perl.


System Requirements

  • O vers. 7, 8, 9, or 10 (Probe with O)
  • O vers. 7 (OwithHydrogens)
  • Probe

Download links

Documentation

ProbeWithO & OwithHydrogens

ProbeWithO incorporates all-atom contacts into the popular model building program O. An O macro and an unix shell script conduit the dot information between Probe and O to give "almost" interactive updates of clashes.

OwithHydrogens is sort of a mess. Its use is not recommended.

If you're using O, then you may be interested in our rotamer library for O.