VVenv file formats

BMERC : needle tools : File formats : VVenv file formats

These file formats are produced by the VVenv programs, and used by various other programs.

Table of contents

1. VVenv file formats
   1. Table of contents
   2. Hyperenv file format
   3. VVenv singleton file format

[still under construction. -- rgr, 21-May-98.]

Note that the first two fields (pdbres1 and pdbres2) do not include a chain ID character. This is a bug; it prevents handling of multichain cores. -- rgr, 26-Jun-98.

Field name	Data format	Description
pdbres1	pdbres	Index and insertion code of the first residue.
pdbres2	pdbres	Index and insertion code of the second residue.
smoothed_dssp_res1	DSSP structure code	Secondary structure code for the first residue.
smoothed_dssp_res2	DSSP structure code	Secondary structure code for the second residue.
pair_res1_window	window	The window through which residue 1 looks at residue 2.
pair_res2_window	window	The window through which residue 2 looks at residue 1.
total_vv_res1	VV percentage	The total (all-window) visible volume within a radius of 14Å, expressed as a percentage of the maximum possible visible volume (as if only the residue's backbone were present).
total_vv_res2	VV percentage	The total visible volume within a radius of 14Å, as for total_vv_res1
cb_res1_w1	integer count	count of beta carbons within 7.5Å that are visible from the first residue through its pair_res1_window.
backbone_res1_w1	integer count	count of backbone heavy atoms within 7.5Å that are visible from the first residue through its pair_res1_window.
vv_res1_w1	VV percentage	The visible volume from residue 1 looking through its pair_res1_window and within a radius of 7.5Å, expressed as a percentage of the maximum possible visible volume.
cb_res2_w2	integer count	count of beta carbons within 7.5Å that are visible from the second residue through its pair_res2_window.
backbone_res2_w2	integer count	count of backbone heavy atoms within 7.5Å that are visible from the second residue through its pair_res2_window.
vv_res2_w2	VV percentage	The visible volume from residue 2 looking through its pair_res2_window and within a radius of 7.5Å, expressed as a percentage of the maximum possible visible volume.
cb_distance	distance (Ångstroms)	Distance between the two beta carbons.

[still under construction. -- rgr, 21-May-98.]

A VVenv singleton file contains the following tab-delimited fields:

Field name	Data format	Description
pdb-index	pdb-index	Chain ID, residue sequence number, and insertion code. [see note 1 below.]
aa	amino acid	Three-letter amino acid name.
ss	(not defined)	Placeholder for the residue's secondary structure code; not used at present, and always "*".
w2_bb_count	integer count	count of backbone heavy atoms that are visible through window 2. [see note 2 below.]
w2_cbeta_count	integer count	count of beta carbons that are visible through window 2.
w3_bb_count	integer count	count of backbone heavy atoms visible through window 3.
w3_cbeta_count	integer count	count of beta carbons visible through window 3.
w4_bb_count	integer count	count of backbone heavy atoms visible through window 4.
w4_cbeta_count	integer count	count of beta carbons visible through window 4.
w2_vv	VV percentage	The visible volume looking through window 2, expressed as a percentage of the maximum possible visible volume. [see note 2 below.]
w3_vv	VV percentage	The visible volume looking through window 3.
w4_vv	VV percentage	The visible volume looking through window 4.

Notes

1. The key field used to contain a pdbres instead of pdb-index value. [Not all of the code has been updated to handle this yet. -- rgr, 24-Jul-98.] [Even then, it was not always in the standard '####A' format. -- rgr, 21-May-98.]

2. In the standard files at BMERC, all counts and visible volume values are computing within a radius of 14 Ångstroms; the actual value depends upon the options given to the calculate-vv-all program.