This menu allows for the display of trigonometric data on molecules. At present it gives distances, close contacts and angles between atoms. It generates display instructions in object distances. Text and dashed lines are drawn in the Id colour defined in the datablock .molec_obj_integer item 8 (see 3.2.12)
dist_define <id 2 atoms>
Identify 2 atoms. A line is drawn between them with the distance. Up to 20 distances can be drawn. The atoms can be identified in a macro by using the Term_id command
trig_reset
Reset and delete the object containing trigonometric information.
trig_refresh
Continuously refresh the trig object. If a marked atom is moving, the trigonometric information is updated. The command can be switched off with Clear_flag or Trig_reset commands.
Neighbour_atom <id an atom> or <mol res atom>
Show neighboring atoms to identified atom. The calculation is repeated so that the contacts of moving atoms get flagged. The distance cut-off is kept in the database in .trig_real . Contacts within the same residue are not calculated
Neighbour_residue <id an atom> or <mol res atom>
Show neighboring atoms to all atoms in the residue of the identified atom. The calculation is repeated so that the contacts of moving atoms get flagged. The distance cut-off is kept in the database in .trig_real Contacts within the same residue are not calculated.
hbonds_mc <id two atoms> or <mol res1 res2>
The hydrogen bonds between main chain atoms within the desired zone are drawn as dotted lines. The bond is made according to a simple energy term defined by Kabsch & Sander (1983) Biopolymers 22, 2577-2637. The cutoff values are 3.5Å in length and 0.5 Kcal/mol in energy. The minimum separation is 3 residues.
hbonds_all <id two atoms> or <mol res1 res2>
The hydrogen bonds between all atoms within the desired zone are drawn as dotted lines. The bond is made according to a trigonometric calculation. The donor-acceptor atoms must be closer than 3.25Å and an angular cut-off of 90°. This option requires that the user database contains a definition of what atoms can act as H-bond acceptors or donors. If not included in the $ODAT/startup.o file, it can be included by reading in $ODAT/residue_dict.o.
phi_psi <id an atom> or <mol res atom>
The phi and psi values for the residue containing each identified atom get displayed in the message window. The command is only applicable to protein molecules. The command stays active so that information about other residues can be obtained by identifying an atom in the residue. It can be reset with Clear_flags.
angle_define <id three atoms>
The angle between 3 identified atoms is calculated and displayed. The atoms can be identified from a macro with the Term_id command.
Activate Dist_define and pick two atoms. A line is drawn between them, with the distance between the two atoms indicated halfway along the line segment. Now activate Move_atom and choose one of the atoms. Choose Trig_refresh, and you will see the distance vector get updated as the atom is moved with the dials.
The distance used as the cutoff for the neighbour calculation is kept in .trig_real as a floating point number.
H-bonds will be drawn as a series of small solid spheres provided a datablock .solid_hbonds is present. The following would draw 7 spheres, each of 0.2Å radius:
.solid_hbonds t 1 12
.2 7