
HELP:
C3DCON is written in Vax FORTRAN and designed to accomplish real-time
crystallographic 3D electron density contouring on a Tektronix-4100 
command series color graphics terminal. The main feature of C3DCON 
is to allow for continuous 3D contouring across the unit cell boundaries
(up to as many cells as the programmed map grid size allows) together 
with structure model overlay. In order to contour across the unit cell
using translation symmetry, the input density map must have a complete 
and unique sampling grid of the unit cell which is assumed to be in 
a-cross, b-down and c-section (e.g. a=0,99,100, b=0,49,50, c=0,69,70).
The above requirement is waived if contouring is confined in the unit cell.

To prepare a 3D electron density file for C3DCON, do the following:

      $ RUN GRAFIT$EXE:FRO_FORIN.EXE
        ......
        JUNK.TMP  !name of map file
        ......
      $ RUN GRAFIT$EXE:FRO_EXPAND.EXE
      $ RUN GRAFIT$EXE:FRO_FFT.EXE
      $ RUN GRAFIT$EXE:MAPACK.EXE
        JUNK.TMP  !same as above
        JUNK.MAP  !output map file for C3DCON
      $ DELETE JUNK.TMP;*

The procedure is the same as for FRODO up to FRO_FFT. Instead of running
MAPAGE.EXE to pack the map as you would for FRODO, run MAPACK.EXE which
packs the electron density file into the byte format required for C3DCON.

By default, C3DCON searches initially for a run file C3DCON.PAR to set up 
the plot and keeps update it every time you exit from the dialogue menu. 
You can use the SAVE command to save the current setup into or the READ 
command to read from a different setup file. The setup file is written
as a keyword-oriented ASCII file you may edit.

To edit plot parameters or setup on screen, enter "AC=parameters" where 
AC is the two letter Access Code assigned to the parameters (e.g. GT=graph 
title). To find out what a particular AC stands for, enter "HELP AC" (e.g. 
HELP GT). Enter "HELP COMMANDS" to get a list of command definitions on 
auxiliary dialogue commands. Enter "GO" to start plotting on screen.

The design of C3DCON also renders itself as a structure model drawing 
routine independent of the presence of an electron density map. Two 
structure models from two different atom files can be plotted on a single
plot screen. C3DCON can essentially read any ASCII atom file using FORTRAN 
run-time format. Before fetching an atom file, you should make sure "L%=", 
"O%=', and "A%=" data fields are given with the right parameters, where "%" 
refers to a number of "6" or "7". The atom list however is not required to 
be in ascending order of residue number. If automatic hydrogen bond search 
is requested and the atom file contains hydrogen atoms, they are assumed 
to immediately follow their host atoms. When entering symmetry information 
from symmetry file, only space-group unique symmetry operators are needed 
(identity operator excluded), and C3DCON searches for all possible 
translation symmetries to fill the sphered model. 
The format of symmetry file is

             x1,y1,z1,t1, x2,y2,z2,t2, x3,y3,z3,t3

one line per operator (e.g. -1 0 0 0  0 1 0 0.5  0 0 -1 0 for P21).

COMMANDS:
Auxiliary dialogue commands for C3DCON:

EXIT/QUIT    : Exit from C3DCON.
GO/PF1       : Start plotting on screen.
HELP/PF2     : Invoke on-line help utility.
REFRESH/PF3  : Refresh the dialogue menu if necessary.
DCL/VMS/PF4  : Spawn a system sub-process.
READ filename: Read a new run setup file (*.PAR), same as F0=filename.
SAVE filename: Save the current plot into a new run setup file.
LOCATE atom  : Locate an atom as the contour box center, where "atom"
               can be specified as e.g. 13CG1 or 13 CG1 or 13,CG1.
TIME         : Display the system clock.
DISTANCE r1,r2,fn: Calculate distances among loaded atoms, where
                   r1 ---  lower distance cutoff for listing.
                   r2 --- higher distance cutoff for listing.
                   fn --- output filename or listing device name.
                          if omitted, it will be listed on screen.
ANGLE r1,r2,fn: Calculate 3 atom angles among loaded atoms, where
                   r1 ---  lower end-point distance cutoff for listing.
                   r2 --- higher end-point distance cutoff for listing.
                   fn --- output filename or listing device name.
                          if omitted, it will be listed on screen.

MENU:
0: Exit to the main menu.
1: Invoke hardcopy making utility.
   If you just get back from auxiliary layout and would like
   to have the changes just made in the layout to show up on
   the hardcopy, redraw the plot before invoking the hardcopy.
2: Invoke auxiliary layout utility.
3: Invoke the dialogue menu.
4: Enter Fkeys mode to toggle graph between visible and invisible.
5: Zoom the graph.
6: Redraw the plot.
7: Toggle graph between mono plot and stereo pair.
8: Edit atom ID and dash bonds, and show atom distances.
9: Rotate the plot and the prompt for delta angles will follow.
$: Spawn a system subprocess.
PF1: Invoke hardcopy making utility without the page setup menu.
PF2: Invoke this help menu.
PF3: Invoke the dialogue menu.
PF4: Spawn a system subprocess.

EDIT:
C3DCON_EDIT_HELP:

To edit the plot, move the crosshair cursor to touch an atom or a bond,
then press one of the following defined function keys:

SPACEBAR: Select atoms for function keys F1,F2,F3,F5,F7. The selected
          atoms are pushed into a 4-atom stack with the latest atom on
          top of the stack. When the 5th atom is selected, the 1st atom
          is discarded.
 F1     : Show distance between the two atoms on top of the atom stack.
 F2     : Show angle among the three atoms on top of the atom stack.
 F3     : Show torsion among the four atoms on the atom stack.
 F4     : Toggle atom ID label.
 F5     : Draw a dash-bond between the two atoms on top of the atom stack.
 F6     : Delete a dash-bond touched by the cursor.
 F7     : Draw distance label between the two atoms on top of the atom stack.
 F8     : Delete a distance label touched by the cursor.
