Editing Slerpy (section)

==Command Reference==

Note that it is essential to understand that slerpy uses the concept of a current or active view. This is the element in the list to which most commands are applied. It is not necessarily the view that is currently visible on the screen. It is advisable to use the sc command frequently to make sure you really know which view your command is being applied to.
 
'''saction ''string'':''' Assoiciates the pymol commands in ''string'' with the current view. ''string'' must be enclosed in quotes and must contain only valid pymol commands separated by semicolons.
 
'''sappend''': Add the currently displayed view at the end of the list of views in slerpy
 
'''sappendaction ''string'':''' Adds the action(s) in ''string'' to the list of actions associated with the current view
 
'''sc''': Go to the slerpy active view
 
'''scrossfade ''startobject, endobject'':''' During the transition from the current view to the next view ''startobject'' will fade out and'' endobject'' will fade in. The two objects must be shown as sticks. They must be objects, not merely selections, as of pymol 0.99.
 
'''sdelaction''': Deletes the action associated with the current view. Be sure you're sure which view you're on before you use this.  This will also delete any actions etc. associated with the view so be careful.
 
'''sdelete''': Remove the slerpy active view from the list of views to be interpolated.
 
'''sdeletesetting: '''Remove the setting interpolation for the current view.
 
'''sdumpactions: '''List all actions by frame.
 
'''sgo ''n'':''' Change the slerpy active view to view ''n''.
 
'''sinsert''': Add the currently displayed view after the slerpy active view.
 
'''sinterpsetting ''setting, selection, startval, endval'' :''' The pymol setting ''setting'' will be interpolated linearly from ''startval'' to ''endval'' during the transition from the current view to the next view. You can only interpolate one setting per transition. This is the hard way to, for example, fade out an object:

 sinterpsetting stick_transparency, lig, 0.0, 1.0

'''slist''': List all views stored for interpolation. Also lists the number of frames in each transition.
 
'''smorph ''startmodel,endmodel'':''' The transition from the current frame to the next frame will consist of one frame per pymol state starting with state ''startmodel'' and ending with state ''endmodel''. Subsequent frames (i.e. from subsequent views) will revert to state 1. The state numbers apply to currently visible objects so you will most likely want to have an object with your starting conformation, an object with your multi-state morphing model, and an object with your final conformation. You would then sgo to the frame where you want the morph to start and add an action to hide the starting conformation object and show the multi-model morphing object, do an smorph 1,30 or whatever the number of states in your morph is, append another frame and give it an action where the multi-state model is hidden and the final conformation is shown.
 
'''sn''': Go to the next view
 
'''sp''': Go to the previous view.
 
'''sread ''filename'':''' Restore all the information written with swrite.  Does not read in the pse file (to avoid inadvertantly writing over some new selections, scenes or whatever).
 
'''srecord''': Records the movie
 
'''sreplace''': Replace the slerpy current view with the currently displayed view.
 
'''sscene''': Add a the currently displayed view after the slerpy active view and create a scene to go with it. The current pymol state, including which objects are displayed and how they are shown will be captured.
 
'''ssetf''': Set the number of frames to use in the transition from the slerpy active view to the next view
 
'''ssetupview ''n'':''' This attempts to make sure that all objects are displayed (or not) as they would be when view ''n'' is arrived at in the movie. It goes through and executes all of the sactions from all preceeding views. For some reason this doesn't always work in complex cases.
 
'''sshow ''n,m'':''' This command records and shows a segment of the movie showing the transitions starting with view n and ending with view m. If the arguments m and n are omitted the transition from the current view to the next view will be shown.
 
'''swrite ''filename'':''' Writes all the information used by slerpy to a file ''filename''.key. It also writes a pymol session file ''filename''.pse containing all of your current objects, selections etc. The format of the .key file is supposed to be human readable and it can be convenient to edit this file rather than using saction over and over. After editing it by hand be sure to do an sread.