3D Analysis  ::  Unix (type) Scripts

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.

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).

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 { 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.

ScoreDotsAtAtom

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

MapVol

awk script to assign volume by atom.

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.

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.