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Download Page for Unix Scripts

On this page are the download links for various scripts written to complement and enhance our software, principally the all-atom contact analysis programs. Some of the scripts require awk or perl, and this is noted in the table. The scripts' functions are summarized below and are also discussed elsewhere on this site. Additionally, if a README-type document is available, it is linked below and will be amongst the download files.


Script Release
date		 Script
type		 Used
with		 README document
(click to read)		 File name
(Click to download)
flipkins
  		 19-Jul-01 perl Reduce, Probe
Prekin, Mage		 readme flipkin.2.4.010719.perl.tar.Z
clashlistcluster
for Linux i386 (RH7.1)		 24-Oct-01 awk Probe
Cluster		 readme clashlist+cluster.1.1.011024.linux.i386.RH71.tgz
clashlistcluster
for irix65		 24-Oct-01 awk Probe
Cluster		 readme clashlist+cluster.1.1.011024.irix65.tar.Z
clashlistcluster
for SunSparc		 03-Jul-01 awk Probe
Cluster		 readme clashlist+cluster.1.1.010703.sun.tar.Z
autobondrot
  		 20-Jul-99 awk Probe, kincontour autobondrot.2.0.990720.script.tar.Z
NAcontacts
  		 01-Nov-00 perl Probe, Bndlst readme nacontacts.2.5.001101.pl.tar.Z
Macro & script
to use Probe in O		 09-Aug-99 O macro
awk script		 Reduce, Probe, O readme probewithO.8.0.990809.script.tar.Z
Scripts to show
hydrogens in O		 04-Feb-00 numerous scripts
& O databases		 Reduce, Probe, O readme OwithHydrogens.1.1.000204.script.tar.Z
PDBCNS
  		 04-May-01 perl readme pdbcns.2.0.010504.perl.tar.Z
scoredotsAtAtom
  		 19-Dec-98 unix shell Kin3Dcont readme scoreDotsAtAtom.1.0.981219.script.tar.Z
mapvol
  		 09-Apr-99 perl Kin3Dcont readme mapvol.1.1.990409.script.tar.Z



Flipkins

This script will generate recommendations as to correct orientation, 'flip', of the sidechains of Asn, Gln and His. Kinemages with animate views of the flips and probe-dots are written. The script served off of this page requires perl. An older version which works with awk is available form our FTP site.



Clashlistcluster

This awk script works with Cluster and Probe, to organize into lists the information about clashes in a molecular model. It requires the binary program, Cluster, which is included in the download; Cluster can also be downloaded separately from its download page. Because Cluster is in the download package, you'll need to pick which of the three tar files matches your OS.



Autobondrot

Autobondrot is a facility in Probe (version 2 or higher) which allows a grid sampling of selected rotatable groups' conformational space for the assessment of packing quality. The awk scripts included in the package below are needed to utilize the autobondrot functionalilty of Probe.



NAcontacts

NAcontacts is a perl script which uses Probe to detail the contacts between nucleic acid layers and/or bases.



PDBCNS

PDBCNS is a perl script which interconverts atom names between the PDB and CNS formats.




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