Hydrogen bonds (HBONDS)
Introduction.
The methodology for the older HBO options.
The methodology for the new HB2 options.
Options that work with potential hydrogen bonds
Listing hydrogen bonds (SHOHBO)
Listing hydrogen bonds (RNGHBO)
Display hydrogens (GRAHYD)
Show and display intra residue hydrogen bonds (SLFHBO)
Show hydrogen bond parameters SHOPAR
Initialize hydrogen bond parameters (INIPAR)
(Re-)set hydrogen bond parameters PARAMS
Donor acceptor distance (DONACD)
Hydrogen acceptor distance (HYDACD)
Angular error over the acceptor (ANGERA)
Angular error over the hydrogen (ANGERH)
Graphics mode of hydrogen bonds (HBOTYP)
Evaluate one hydrogen bond (ONEHBO)
Determine hydrogen bonds for one atom (1ATHBO)
Determine hbonds in a sphere (SPHHBO)
Hydrogen bonds as function of secondary structure (HSTHBO)
Backbone or sidechain hydrogen bonds (BSSHBO)
Hydrogen bonds for one residue (1AAHBO)
Selected hydrogen bonds (FILHBO)
options that use optimised hydrogen bonds
Initialize the HB2 routines with the current soup (HB2INI)
Reset the coordinates to original values (HB2RES)
Find the best hydrogen bond network (HB2NET)
Create new PDB file including hydrogen atoms (HB2MAK)
Show HB2 hydrogen bonds graphically (HB2GRA)
List HB2 hydrogen bonds textually (HB2LIS)
Show list of flipped residues and unusual groups (HB2LFR)
Show list of not donating buried donors (HB2LUH)
Show list of not accepting buried acceptors (HB2LUA)
Show list of all potential acceptors for all donors (HB2LPA)
Show list of all affected donors for all ambiguities (HB2LAD)
Show some extra statistics (HB2XST)
Add a wanted hydrogen bond (HB2AWB)
Clear list of wanted hydrogen bonds (HB2CWB)
Show list of bifurcated hydrogen bonds (HB2LBF)
Set the flip penalty (HB2SPN)
The H-bond energy (HB2ENE)
Activating more commands (MORE)
Hidden commands
(BBSHBO)
(HBOBBS)