Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_23 DockVision at MUSC.

1) Running DockVision from other than a Workstation will require that 
   you have x-server software on the PC or workstation.

2) Running DockVision at MUSC will require that you add a line to your
   ".cshrc" file. That line should read:

   source /usr/common/bcr/DockVision/startup.csh

3) After you have added this line to your .cshrc file, then you can
   type " source .cshrc" or logout and then login again. At this
   point your unix environment will be properly set up. Then
   you need merely to type

   DockVision

   An x-terminal window will open and you may commence setting
   up a docking run.



4) The window that appears has a series of red filled or bordered
   rectangles. As you supply appropriate information, the red 
   fields will change to green. You begin by supplying a run name
   and then selecting ligand and target molecules.
   
5) DockVision reads PDB format 'target' and 'ligand' files. The
   program is fairly tolerant of various PDB file variants but
   you may have to fix up your PDB file to make it palatable to
   DockVision. 

6) The Ligand, Target, Flexibility, Grid, Options and Research
   rectangles all open interactive windows where you supply information
   to configure the program for running. When you start its best to
   just use the Research Potential Function.

7) Under the MODE menu you can select various operating modes for
   DockVision and several utility programs and job control features.
   DockVision can run a Monte-Carlo docking procedure (RESEARCH),
   a genetic algorithm docking procedure (GAMMA),and  a database search 
   program (RSDB). The TOOLS mode opens a window with access to several
   set-up and analysis tools.
                                                                                                                                                                                    
8) By selecting the "next" button in the lower right of the Dockvision 
   window you can sequentially provide the information required for a
   DockVision analysis. Entering a run Name,selecting a ligand and then
   a target and a Potential Function completes the first page. The next
   button opens a new window.

9) The ligand may either be flexible of rigid.

10) The options button opens a new window showing that a CONSTRAINT file 
    and a Schedule file must be read(load) or configured (built). For 
    starting, a constriant centered at 0,0,0 and a radius of 5-50
    Angstroms is useful. The default Schedule settings are a useful
    start as well. Both may be refined for more thorough searches in
    particular regions.

11) When DockVision has all the information it needs, pressing the
    run button initiates the docking. The calculation of the GRID and
    computation of conformations for flexible ligand conformations
    can be time-consuming. Once the GRID and conformations have been 
    calculated, Dockvision can quickly be reset to evaluate various
    run parameters.