:: DESCRIPTION
ClashScore generate a percentile plot of ClashScore versus Resolution like that found in the X-Ray Verification Task Force’s recommendation to wwPDB.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ClashScore is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
BndLst is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
AtVol 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.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
AtVol is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
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”
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Cluster is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
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.
They are used to generate 2D or 3D contour maps in kinemage format. The programs kin2Dcont and kin3Dcont produce contour plots from tables of values and their 2-D or 3-D coordinates. If the data is scattered in space, the programs can smooth it and produce what is essentially a histogram in two or three dimensions. Evenly sampled data values can also be contoured, as well as data which is periodic, for example when the dimensions are angles with 360 deg the same as 0 deg.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
A Decomposable Algorithm for Contour Surface Display Generation, Michael J. Zyda, ACM Transactions on Graphics, Vol. 7, No. 2, April 1988, Pages 129-148.
Kin2Dcont & Kin3Dcont are free softwares available under the terms of its own BSD-style license.
:: DESCRIPTION
Dangle an updated and more general version of our program Dang in that it reads coordinates from a Protein DataBank (PDB) coordinate file for either protein or nucleic acid and generates geometric measurements for each residue. It is different from Dang in that Dangle: is Java-based, includes the capability of reporting deviations from ideal geometry as well as measurement values, and has a very flexible input syntax for specified the measurements desired. Dangle output is given as colon-delimited values, one line per residue. It is designed for facile use in scripts, and is the usual source of input for Suitename, either to generate the data for MolProbity’s multi-criterion table or in individual command-line use.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Dangle is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Dang is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Remediator converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2). Remediator is available as a Perl or Python script. The scripts should work on any type of computing platform, as long as your operating system has the appropriate framework.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Remediator uses the remediated Chemical Component Dictionary as its “rosetta stone” for conversion.
Remediator is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Suitename is a new C program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development
From dihedral-angle input for a specific RNA structure (usually from Dangle), Suitename categorizes the RNA backbone geometry of each suite (the sugar-to-sugar version of a residue) either as an outlier (“!!”) or as belonging to one of the 53 defined conformer bins.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Suitename is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.
::DEVELOPER
Xueyi Wang & Prof. Jack Snoeyink
Richardson Lab
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
RNABC is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone”. Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)
RNABC is free software available under the terms of its own BSD-style license.
