Slerpy - Revision history

Bell: 50 revisions

2014-03-28T03:55:43Z

50 revisions

Newacct at 08:01, 1 March 2010

2010-03-01T08:01:34Z

Newacct at 00:58, 7 February 2010

2010-02-07T00:58:52Z

Newacct at 11:55, 17 December 2009

2009-12-17T11:55:50Z

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Newacct at 08:11, 27 November 2009

2009-11-27T08:11:37Z

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Splette: /* Why is it called slerpy? */

2007-06-15T02:00:52Z

Why is it called slerpy?

Splette: /* Morphing and multi-state models */

2007-06-15T02:00:04Z

Morphing and multi-state models

Splette: /* slerpy.py */ added line in readKeyViewFile of slerpy.py to prevent error message when you try reading key file with "sread myfile.key" rather than "sread myfile"

2007-06-14T04:12:56Z

slerpy.py: added line in readKeyViewFile of slerpy.py to prevent error message when you try reading key file with "sread myfile.key" rather than "sread myfile"

Joelbard: /* slerpy.py */

2007-01-08T04:05:15Z

slerpy.py

Joelbard: /* slerpy.py */

2007-01-02T03:14:43Z

slerpy.py

@@ Line 975: / Line 975: @@
          Y = (M[2] - M[6])*S
          Z = (M[3] - M[1])*S
      else:
-         if M[0] > M[4] and M[0] > M[8]:
+         S = sqrt( 1.0 + M[8] - M[0] - M[4]) * 2
-            S = sqrt( 1.0 + M[0] - M[4] - M[8]) * 2
+         X = (M[2] + M[6])/S
-            X = 0.25 * S
+        Y = (M[5] + M[7])/S
-            Y = (M[1] + M[3])/S
+        Z = 0.25 * S
-            Z = (M[2] + M[6])/S
+        W = (M[1] - M[3])/S
      return [X,Y,Z,W]

@@ Line 540: / Line 540: @@
      #find a free scene name
      i = 1
-    found = 1
+     while True:
          for sname in scenes.values():
              print "|"+sname+"|"
              if sname == "slerpy_"+str(i):
                  break
          else:
              break
      newname = "slerpy_"+str(i)

@@ Line 169: / Line 169: @@
 ==Why is it called slerpy?==
-slerp is an acronym of sorts for spherical linear interpolation.  The transition between two views approximates spherical linear interpolation of the their camera positions using quaternions.  See the Wikipedia [[http://en.wikipedia.org/wiki/Slerp article]] on slerps.
+slerp is an acronym of sorts for spherical linear interpolation.  The transition between two views approximates spherical linear interpolation of the their camera positions using quaternions.  See the Wikipedia [http://en.wikipedia.org/wiki/Slerp article] on slerps.
 =Script Files=

@@ Line 111: / Line 111: @@
 Morphs and multi-conformation models are represented in pymol as single objects with multiple states.  Cycling through the states as an animation is very straightforward in pymol.  Slerpy allows you to include this animation over the states of an object as a transition between slerpy views within the context of larger movie.  This is done using the ''smorph'' command (see [[#Command Reference|Command Reference]]).  ''smorph'' allows you to specify the starting and ending pymol state numbers to use during the transition from the current to the next view.  It will often be appropriate to have the movie continue after the morph using the final state of the morphing model, that is, the conformation to which you morphed.  Since the default for a typical slerpy view is to show the first state of an object, you'll probably need to have available, in addition to your multi-state model, a single-state object containing the final conformation.  You can then hide the multistate object and show the single-state final conformation as an action associated with the final view of your morphing sequence.
-To generate morphs you can use the [[http://www.delanoscientific.com/rigimol.html rigimol]] program provided by Warren as part of the incentive pymol package for subscribers or use [[http://alpha2.bmc.uu.se/usf/mol_morph.html lsqman]] from Gerard Kleywegt.
+To generate morphs you can use the [http://www.delanoscientific.com/rigimol.html rigimol] program provided by Warren as part of the incentive pymol package for subscribers or use [http://alpha2.bmc.uu.se/usf/mol_morph.html lsqman] from Gerard Kleywegt.
 ==Command Reference==

@@ Line 667: / Line 667: @@
      fades = {}
      scene_counter = 0
-−
      keyviewfile = open( filename + ".key", 'r' )
      viewstrings = keyviewfile.readlines()

← Older revision	Revision as of 03:55, 28 March 2014
(No difference)

@@ Line 846: / Line 846: @@
              if actions.has_key(i):
                  mdo_cmd += actions[i]+";"
-             mdo_cmd += "set_view("+str(views[i])+")"
+             #mdo_cmd += "set_view("+str(views[i])+")"
              print mdo_cmd
              cmd.mdo(start_frame, mdo_cmd)

@@ Line 427: / Line 427: @@
      print "New view:"
      print_view( cur_view )
-     print "Inserted view at with index", cur_index, "and a 50 frame transition"
+     print "Inserted view with index", cur_index, "and a 50 frame transition"
 def append_view():
@@ Line 529: / Line 529: @@
      views.insert( cur_index, [cv for cv in cur_view] )
      frames.insert( cur_index, 50 )
      #deal with dictionaries
@@ Line 565: / Line 561: @@
      print "New view:"
      print_view( cur_view )
-     print "Inserted view at with index", cur_index, "and a 50 frame transition"
+     print "Inserted view with index", cur_index, "and a 50 frame transition"
      print "Added scene",newname
@@ Line 874: / Line 870: @@
          ftot += nframes
          if models.has_key(i):
-                            setcommand += " " + models[i] + " "
+            setcommand += " " + models[i] + " "
          else:
              setcommand += " 1 x%i" % nframes