If you use these programs, you may want to cite:
Neil R Voss, Mark 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.
-DistCheck = Double for Distance Check (default = 8.5) -i = PDB input file for reading (default = ./in.pdb) -method = Double specifying method to use in calculating volumes (default = 4)
Options:
- Normal Voronoi (bisection)
- Richards' Method B
- Radical Plane
- Simplified Method B
-probe = Probe value in Angstroms (default = 1.4) -residue-file = File containing definition of all residues (default = ./resi-defs.def) -stdvols = File containing standard volumes of all atom types (173 for proteins) (default = ./stdvol173.def) -SurfThresh = Double specifying cutoff surface area (default = 3.0) -types-file = File containing atom type and radius (default = ./atom-defs.def) -VolMaxDist = Double for Maixmum Distance in calculating Volume (default = 64.0) > = Pipe to an 'output file' to grab output (default = stdout)
number_ = Atom Number (taken from PDB file) resnum = Residue Number (taken from PDB file) chain = Chain number or letter (taken from PDB file) resname = Residue Type (taken from PDB file) atname = Atom Type (taken from PDB file) typenum = Type Number corresponding to a particlar typenam typenam = Type Name (taken from atom-defs.dat file) covrad = Covalent Radius of Atom (taken from atom-defs.dat file) vdwrad = Van Der Waals Radius of Atom (taken from atom-defs.dat file) surface = Surface Area Calculated by program volume = Volume Calculated by program refvol = Reference Volume packeff = volume divided by the refvol goodbad = Rating of Goodness
Rules:
- [OK] Surface Area is less than SurfThresh
- possible Surface Area is greater than SurfTresh and Volume Calculation was Feasible
- bad Volume was not closed and therefore impossible
To be documented...
-Fixed = Filename of Fixed Structure -Moving = Filename of Moving Structure -Output = Filename to output (transformed) Moving Structure -Selection = Filename of CA Selections ( '-' = stdin ) -VerboseDumpRT = Print out transformation with rotation angle and axis -SimpleDumpRT = Print out transformation in a simple form -DoTransRot = Apply transformation to coordinates -SelectAll = Select All Atoms -VerifySelect = Dump the selected atoms for verification -CompareCoordinates = Compare CAs Selection File Format : File = StrucSel-for-fixed StrucSel-for-moving StrucSel = Range { [range] } Range = from-integer to-integer chain-char (If chain is '_' or NULL, chain is ' ') Example : Fixed { 1 10 A 20 30 A } Moving { 10 20 40 50 }
Rotation[3,3] - 3x3 rotation matrix Translation[3] - translation vector RMS[1] - Ca rms in Å
Neil R Voss, Mark 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.
nVradii.exe -method [1-5] -output_format [1] -outname [foo] -pdb_dir [dir] -res_file [rd_file] -surf_thresh [#] -types_file [ad_file] -weed_level [AcHstw] -debug -debug1 -test < input-pdbfile-list
list of pdb filenames to analyze [identifier & suffix of .pdb]. (for examples of these lists and results go here).
-debug - turns on lots of print statements for debugging purposes. some debugging output to STDOUT, but most to STDERR. -debug1 - currently not used, although at one time used for debugging. -method [1-5] - this sets how the plane between atoms is calculated. it can be done one of 5 ways. the default is 2. Descriptions for each are below:
1 - Bisection (Richard's Method A). 2 - Richard's Method B. 3 - Radius specified in the atom definition file is extended by some probe value. this is akin to a SASA calculation. 4 - Richard's Method B for all covalent and non-covalently touching atoms. 5 - The dividing plane is set at at distance r defined by r = 1 - R/D, where R is the atom's radius and D is the distance to its neighbor. -output_format [1] - this specifies which output format to use. it is here so that results could be easily compared to old runs. the default is to output in the format shown on the data README page. -outname [foo] - this sets the portion of the name for the output files that are explained below. if no name is specified, the program uses the name of the types_file, otherwise it is nVradii_out. -pdbdir [dir] - this sets the path for where to find the pdb files. the program uses the directory pdb/ as its default. -res_file [rd_file] - this sets where to find the the residue definitions file, specified by rd_file (default is $HOME/lib/default-residue-defs.dat). downloadable examples & explanations of residue definition files can be found on the data README page. -surf_thresh [#] - # specifies the cutoff value for the surface area atom filtering. used in conjuction with the s & t specifiers in -weed_level option. -types_file [ad_file] - this sets where to find the the atom definitions file, specified by ad_file (default is $HOME/lib/default-atom-defs.dat). downloadable examples & explanations of atom definition files can be found on the data README page. -test - currently not used, although at one time used for debugging. -weed_level [AcHstw] - this sets up the various atom filtering methods. for an explanation of what has been used in the papers, go here. each letter in the brackets activates a different type of atom filtering: the atom filtering codes used in the papers are different then those used here. the following combinations will reproduce the the atom filtering done in the paper (ordered from least to most restrictive):
A - atoms touching HET atoms. c - atoms whose volume changes when the caclculation is done with and without the HET atoms in the pdb file. H - all HET atoms. s - atoms with a exposed surface area above some cutoff values specified by the -surf_thresh [#] option. t - used in conjunction with the s atom filtering for those atoms touching exposed atoms. w - waters included in the pdb file.
base - no options [default] B- - wc BL- - ws w/ the default -surf_thresh BLW - c BD - st w/ the default -surf_thresh
STDOUT - if -debug option is used, debugging print statements, otherwise nothing. STDERR - log file and debugging print statements if -debug option is used. foo.a-surf - surface areas for the 173 amino acid atoms and sums for each residue. foo is the root name specified by the -outname option explained above. foo.res-surf - surface area of the 21 amino acids in one file. foo.a-vols - volumes for the 173 amino acid atoms and sums for each residue. foo is the root name specified by the -outname option explained above. Examples of these files can be found on the data README page. foo.res-vols - volumes of the 21 amino acids in one file. Examples of these files can be found on the data README page.