File: auto_stuff.txt
Last modified: 17-jan-2003


Menu block "AUTO_STUFF" contains items, which do things, they are set for, automatically. User has to choose the range of a function application: working segment, key active or clicked history atoms.

Menu block "AUTO_STUFF" is loaded with


Redefines coordinates of the peptide bond between two clicked residues to ideal trans-peptide bond values. It fixes any mess that a minimizer run can not handle.

MAIN_CMDS:auto_stuff_fix_pept.cmds does it.


Fixes a side chain conformation of chosen residues by looking for the nearest best conformation,

MAIN_CMDS:auto_stuff_side.cmds with the opion "ASIS does it.


Fixes a side chain conformation of chosen residues by choosing the most extended conformation.

MAIN_CMDS:auto_stuff_side.cmds with the opion "EXTEND does it.


Finds instantaneoulsy optimal peptide bonds orientation of selected "active" residues. The Algorithm checks non-bonding interactions with neighboring CA and CB atoms, secondary structure pattern and electron density map fit. All three terms are independently scaled and added together forming the scoring function.

The default macro MAIN_CMDS:auto_stuff_find_pept.cmds may need adjustment to your needs by a different "SECONDARY" scale and "MAP" assignment. By default the currently chosen map for contouring is used. Higher resolution gives higher scale to the density, while lower resolution maps are scaled down as carbonyls can not really be revealed by them, the non-bonding and secondary structure terms thus prevail.

The secondary structure pattern is recognized on the basis of CA and CB atoms of neighboring residues. Currently there are 7 possible secondary structure targets. Recognition process is absed on dihedral angle of four neighboring residues using CA atoms (CA-1234), dihedral angle of two adjacent two residues using CB-CA-CA-CB atoms and distances between 1-3 and 1-4 CA atoms. Standard values are shown below and can currently not be modified.

          B-anti  B-par   Alpha   3-10   Al-left  coll   p-pro
 CA-1234  178.7   177.5    49.8    71.1   -67.8  -82.5 -110.5
 CBA-CAB  178.7   178.4    71.1    80.4   -92.1 -123.1 -106.0
 CA 1-3    6.90    6.51    5.47    5.26    5.25   6.55   6.60
 CA 1-4   10.47    9.96    5.20    5.63    5.47   8.54   9.37

After recognizing a secondary structure target "CO" and "NH" groups are used to calculate dihedral energy terms with CA-CB or CA-CA atoms. The first two lines are used when "CB" atom is present in a residue, wheras neighboring "CA" atoms are used in the cases of a glycine.

 OC-CACB   77.4    55.4  -114.6   -75.6   -27.6   90.4   92.4
 HN-CACB  -81.7   -61.7     9.3   -13.7   117.5  -18.7  -22.7
 OC-CACA  -56.7   -81.9   111.7   147.2  -136.6  -64.9  -45.6
 HN-CACA   58.5   -82.3   114.7   102.8  -109.9  148.3  112.9


Fits the side chain atoms into the density of the current active map.

MAIN_CMDS:auto_stuff_side.cmds with the opion "FIT does it.


"RIG_RESI" breaks residues into fragements as are rings, carboxylic and guanidinium groups and man chain and fits each of them into the active electron density map. After fit check the geometry and "minimize". Should be used with caution, because groups can move uexpectidly far away.

MAIN_CMDS:auto_stuff_rig_resi.cmds does it.


Defines weights of atoms by checking their positioning in a density map (MAP_2FOFC or MAP_FO). It starts with the root atom "CA" and proceedes along the main and side chain. The first atom outside the density contour leaves the rest of the chain weighted with 0 too.

Click on "RE_IMAGE" colors the regions outside the map with green.

The default macro is MAIN_CMDS:auto_stuff_weight.cmds which calls the actual automatic weighting procedure


Defines weights by considering the positions of individual atoms in the actiove density map. Weight 0 is set to atoms lating below the contour level, whereas the ones lying in the regions above or equal to the contour level is seto to 1.0.

Click on "RE_IMAGE" colors the atoms outside the map with green.

MAIN_CMDS:auto_stuff_weight_atom.cmds does it.