README
shell (sh) scripts used with nVradii.exe

What is this?

This README describes the perl scripts process some of the output files from the nVradii.exe program.

The program nVradii.exe creates 6 files (for more detail on nVradii.exe go here). Of the six, these programs process the two files with volume or surface area data for the 173 raw residue atoms: *.vol173.* & *.surf173.* files, where all 173 are different from each other. In brief, CollapseToAtomTypes.pl acts on either of the two aforementioned output files to find the results for the N atom types used. ExpandFromAtomTypes.pl uses these N atom types to recreate the 173 residue atom file. This predicted 173 residue atom file is different from the raw 173 residue atom file in that not all values are unique. The GetAAValFrom173file.pl processes either of the 173 residue atom files to extract just the total residue volumes. (For more detail see below.)

If you use these programs, you may want to cite:

NR Voss, MB Gerstein
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
J Mol. Biol. v346(2): 2005, pp 477-492.

NOTE :: All examples below shown on files contain volumes for consistency with the naming conventions used in the volume data files. However, these work just as well for files containing surface area data.

Collapsing the Raw 173 Residue Atoms into N Atom Types

CollapseToAtomTypes.pl (to get script)

Form: CollapseToAtomTypes.pl < [*.vol173.*] > [*.atom-vols.*]

Description:

Input File   : [*.vol173.*] - raw 173 residue atom output file of volumes from 
               nVradii.exe.

Output File  : [*.atom-vols.*] - volumes collapsed into N atom types.

Dependencies : looks for [*.resi-defs.*] defined at the top of the [*.vol173.*] 
               (usw. on the first line).  Note, the path must be correct to the 
               [*.resi-defs.*].  If not, the script will not find the file and 
               will then bomb out.

Expanding N Atom Types to Predicted 173 Residue Atoms

ExpandFromAtomTypes.pl (to get script)

Form: ExpandFromAtomTypes.pl < [*.atom-vols.*] > [*.vol173predicted.*]

Description:

Input File   : [*.atom-vols.*] - volumes collapsed into N atom types.

Output File  : [*.vol173predicted.*] - predicted 173 residue atom file of volumes.

Dependencies : looks for [*.resi-defs.*] defined at the top of the [*.atom-vols.*] 
               (usw. on the first line).  Note, the path must be correct to the 
               [*.resi-defs.*].  If not, the script will not find the file and 
               will then bomb out.

Extracting Amino Acids from 173 Residue Atom File

GetAAValFrom173file.pl (to get script)

Form: GetAAValFrom173file.pl < [*.vol173.*] or [*.vol173predicted.*] > [*.residue-vols.*]

Description:

Input File   : [*.vol173.*] or [*.vol173predicted.*] - either the raw or the predicted 
               173 residue atom file of volumes.

Output File  : [*.residue-vols.*] - residue volumes foreach amino acid.

Dependencies : None.

Further Links

Examples of the data