ViewDock

ViewDock is a UCSF Chimera extension for viewing outputs from several docking software packages. There is a tutorial on the Chimera web pages.

Keyboard shortcuts

Using ViewDock requires a fair amount of clicking and mouse movement. To reduce these you can use this Chimera accelerators script, written by Tom Goddard (Chimera user list discussion):

def register_accelerators():                                                       
                                                                                   
  from Accelerators import standard_accelerators                                   
  standard_accelerators.register_accelerators()                                    
                                                                                   
  from Accelerators import add_accelerator                                         
  add_accelerator('cd', 'Mark current View Dock compound deleted', vdock_delete)
  add_accelerator('cx', 'Mark current View Dock compound purged', vdock_purged) 
  add_accelerator('cv', 'Mark current View Dock compound viable', vdock_viable) 
  add_accelerator('cn', 'Move to next View Dock compound', vdock_next)             
  add_accelerator('cp', 'Move to next View Dock compound', vdock_previous)         
                                                                                   
def vdock_delete():                                                                
    from ViewDock.Compound import Compound                                         
    vdock_set_state(Compound.Deleted)                                              
                                                                                   
def vdock_purged():                                                                
    from ViewDock.Compound import Compound                                         
    vdock_set_state(Compound.Purged)                                               
                                                                                   
def vdock_viable():                                                                
    from ViewDock.Compound import Compound                                         
    vdock_set_state(Compound.Viable)                                               
                                                                                   
def vdock_set_state(state):                                                        
    vd = vdock_dialog()                                                            
    if vd:                                                                         
        vd.results.setSelectedState(state)                                         
        vd._reloadCompounds()                                                      
                                                                                   
def vdock_next():                                                                  
    vdock_step(1)                                                                  
                                                                                   
def vdock_previous():                                                              
    vdock_step(-1)                                                                 
                                                                                   
def vdock_step(step):                                                              
    vd = vdock_dialog()                                                            
    if vd:                                                                         
        r = vd.results                                                             
        csel = r.selected                                                          
        if csel:                                                                   
          c = csel[0]                                                              
          clist = r.compoundList                                                   
          i = clist.index(c)                                                       
          if i+step < len(clist) and i+step >= 0:                                  
            nextc = clist[i+step]                                                  
            vd.results.setSelected([nextc])                                        
                                                                                   
def vdock_dialog():                                                                
    from ViewDock import ViewDock                                                  
    from chimera import extension                                                  
    for vd in extension.manager.instances:                                         
        if isinstance(vd, ViewDock):                                               
            return vd                                                              
    return None       

To use, enable Chimera keyboard shortcuts and load the new file.

Accelerators "cv" (Viable), "cd" (Delete), "cx" (Purge), work like clicking the radio buttons in the ViewDock dialog box - they change the status of the selected compound. Accelerators "cn" and "cp"

ChimeraX/ViewDockX

There is an equivalent tool ViewDockX in the next generation visualisation tool ChimeraX.