Dynamic mesh - Revision history

Pyadmin: 4 revisions

2014-03-28T01:43:49Z

4 revisions

Speleo3: moved to github

2012-08-30T16:15:41Z

moved to github

TakanoriNakane: Supported map_auto_expand_sym

2012-08-25T11:59:54Z

Supported map_auto_expand_sym

TakanoriNakane: Wizard > Density

2012-08-24T00:25:36Z

Wizard > Density

TakanoriNakane: Created page with "'''dynamic_mesh''' displays isomesh around the center of the view. When the view is moved, the isomesh will be updated automatically. You can also change contour level by Pag..."

2012-08-23T02:19:01Z

Created page with "'''dynamic_mesh''' displays isomesh around the center of the view. When the view is moved, the isomesh will be updated automatically. You can also change contour level by Pag..."

New page

'''dynamic_mesh''' displays [[isomesh]] around the center of the view. When the view is moved, the isomesh will be updated automatically.
You can also change contour level by PageDown/PageUp keys. This script is intended to implement interface similar to Coot for examing electron density maps.

== Usage ==

dynamic_mesh mapname [, level [, radius]]

where

map_name = string: name of volumetric object(map) to display
level = float: contour level of isomesh {default: 0.8}
radius = float: radius of isomesh around the center of the view {default: 8}

== Example ==

<syntaxhighlight lang="python">
fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1
run dynamic_mesh.py
dynamic_mesh 1hwk_map
show sticks, resn 117
show ribbon
zoom chain A and resn 117
</syntaxhighlight>

Note: On PyMOL <= 1.4, you have to download the electron density map from the Uppsala Electron Density Server manually.

== Script ==

<syntaxhighlight lang="python">
# Dynamic Mesh by Takanori Nakane, License: BSD-2 Clause
# version 0.11: 20120823

'''
This script was tested on PyMOL 1.2 and 1.5.

Example:

fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1
run dynamic_mesh.py
dynamic_mesh 1hwk_map
show sticks, resn 117
show ribbon
zoom chain A and resn 117

Note: On PyMOL <= 1.4, you have to download the electron density
map from the Uppsala Electron Density Server manually.
'''

from pymol.callback import Callback
from pymol import cmd

class DynamicMesh(Callback):
def __init__(self, meshname, level = 0.8, radius = 8):
self.center = cmd.get_position()
self.level = level
self.radius = radius
self.mesh = meshname
cmd.set("auto_zoom", 0)
cmd.pseudoatom("__center__", pos = self.center, quiet = 1)
cmd.hide("everything", "__center__")
cmd.set_key("pgup", self.contour_plus)
cmd.set_key("pgdn", self.contour_minus)
# TODO: Where should I unregister them?
self.update()

def contour_plus(self):
self.level += 0.1
print "Map level: " + str(self.level)
self.update()

def contour_minus(self):
if (self.level < 0.15):
return
self.level -= 0.1
print "Map level: " + str(self.level)
self.update()

def update(self):
self.center = cmd.get_position()
cmd.alter_state(0, "__center__", "(x, y, z) = p", space={'p': self.center})
cmd.isomesh("dynamic_mesh", self.mesh, self.level, "__center__", carve = self.radius)

def __call__(self):
tmp = cmd.get_position()
r = (self.center[0] - tmp[0]) * (self.center[0] - tmp[0]) + \
(self.center[1] - tmp[1]) * (self.center[1] - tmp[1]) + \
(self.center[2] - tmp[2]) * (self.center[2] - tmp[2])
if (r > 0.3): # increase this number if it is too slow
self.update()

def get_extent(self):
tmp = cmd.get_position()
return [[tmp[0] - self.radius, tmp[1] - self.radius, tmp[2] - self.radius], \
[tmp[0] + self.radius, tmp[1] + self.radius, tmp[2] + self.radius]]

def dynamic_mesh(meshname, level = 0.8, radius = 8):
'''
DESCRIPTION

Make 'dynamic' mesh from volumetric data such as electron density map.
The mesh will dynamically follow the center of the view.
Contour leveo of isomesh can be changed by PageDown and PageUp keys.

NOTE: Crystallographic operations will not be applied to the map.
Only pre-calculated volume can be displayed.

USAGE

dynamic_mesh mapname [, level [, radius]]

ARGUMENTS

map_name = string: name of volumetric object(map) to display

level = float: contour level of isomesh {default: 0.8}

radius = float: radius of isomesh around the center of the view {default: 8}

SEE ALSO

isomesh
'''

cmd.delete("dynamic_mesh") # TODO: support multiple meshs
cmd.delete("dymesh_callback")
cmd.load_callback(DynamicMesh(meshname, float(level), float(radius)),'dymesh_callback')

cmd.extend('dynamic_mesh', dynamic_mesh)
cmd.auto_arg[0]['dynamic_mesh'] = [ cmd.map_sc, 'map object', ', ']
</syntaxhighlight>

== See Also ==

* [[isomesh]]
* [[get_position]]
* Coot http://lmb.bioch.ox.ac.uk/coot/

[[Category:Script_Library]]
[[Category:UI_Scripts]]

@@ Line 1: / Line 1: @@
 '''dynamic_mesh''' displays [[isomesh]] around the center of the view. When the view is moved, the isomesh will be updated automatically.
 You can also change contour level by PageDown/PageUp keys. This script is intended to implement interface similar to Coot for examing electron density maps.
@@ Line 6: / Line 13: @@
 == Usage ==
-  dynamic_mesh mapname [, level [, radius [, sym_source]]]
+  dynamic_mesh map_name [, level [, radius [, name [ sym_source ]]]]
-where
+== Arguments ==
- map_name = string: name of volumetric object(map) to display
+* map_name = string: name of volumetric object(map) to display
- level = float: contour level of isomesh {default: 0.8}
+* level = float: contour level of isomesh {default: 1.0}
- radius = float: radius of isomesh around the center of the view {default: 8}
+* radius = float: radius of isomesh around the center of the view {default: 8}
- sym_source = string: name of object from which symmetry
+* name = string: name of mesh object {default: dynamic_mesh}
-                  information is derived {default: None}
+* sym_source = string: name of object from which symmetry information is derived {default: map_name}
 == Example ==
@@ Line 29: / Line 36: @@
 Note: On PyMOL <= 1.4, you have to download the electron density map from the Uppsala Electron Density Server manually.
 == See Also ==
@@ Line 152: / Line 47: @@
 [[Category:Script_Library]]
 [[Category:UI_Scripts]]

← Older revision	Revision as of 01:43, 28 March 2014
(No difference)

@@ Line 6: / Line 6: @@
 == Usage ==
-  dynamic_mesh mapname [, level [, radius]]
+  dynamic_mesh mapname [, level [, radius [, sym_source]]]
 where
@@ Line 13: / Line 13: @@
   level = float: contour level of isomesh {default: 0.8}
   radius = float: radius of isomesh around the center of the view {default: 8}
 == Example ==
@@ Line 20: / Line 22: @@
 fetch 1HWK, 1hwk_map, type=2fofc, async=1
 run dynamic_mesh.py
-dynamic_mesh 1hwk_map
+dynamic_mesh 1hwk_map, sym_source=1hwk
 show sticks, resn 117
 show ribbon
@@ Line 32: / Line 34: @@
 <syntaxhighlight lang="python">
 # Dynamic Mesh by Takanori Nakane, License: BSD-2 Clause
-# version 0.11: 20120823
+# version 0.2:  20120825
-−
 '''
 This script was tested on PyMOL 1.2 and 1.5.
-−
 Example:
-−
 fetch 1HWK, async=1
 fetch 1HWK, 1hwk_map, type=2fofc, async=1
 run dynamic_mesh.py
-dynamic_mesh 1hwk_map
+dynamic_mesh 1hwk_map, sym_source=1hwk
 show sticks, resn 117
 show ribbon
 zoom chain A and resn 117
-−
 Note: On PyMOL <= 1.4, you have to download the electron density
 map from the Uppsala Electron Density Server manually.
 '''
-−
 from pymol.callback import Callback
 from pymol import cmd
 class DynamicMesh(Callback):
-     def __init__(self, meshname, level = 0.8, radius = 8):
+     def __init__(self, meshname, level, radius, sym_source):
          self.center = cmd.get_position()
          self.level = level
@@ Line 62: / Line 64: @@
          cmd.set("auto_zoom", 0)
          cmd.pseudoatom("__center__", pos = self.center, quiet = 1)
          cmd.hide("everything", "__center__")
          cmd.set_key("pgup", self.contour_plus)
@@ Line 67: / Line 72: @@
          # TODO: Where should I unregister them?
          self.update()
-−
      def contour_plus(self):
          self.level += 0.1
          print "Map level: " + str(self.level)
          self.update()
-−
      def contour_minus(self):
          if (self.level < 0.15):
@@ Line 79: / Line 84: @@
          print "Map level: " + str(self.level)
          self.update()
-−
      def update(self):
          self.center = cmd.get_position()
          cmd.alter_state(0, "__center__", "(x, y, z) = p", space={'p': self.center})
          cmd.isomesh("dynamic_mesh", self.mesh, self.level, "__center__", carve = self.radius)
-−
      def __call__(self):
          tmp = cmd.get_position()
@@ Line 92: / Line 97: @@
          if (r > 0.3): # increase this number if it is too slow
              self.update()
-−
      def get_extent(self):
          tmp = cmd.get_position()
          return [[tmp[0] - self.radius, tmp[1] - self.radius, tmp[2] - self.radius], \
                  [tmp[0] + self.radius, tmp[1] + self.radius, tmp[2] + self.radius]]
-−
-def dynamic_mesh(meshname, level = 0.8, radius = 8):
+def dynamic_mesh(meshname, level = 0.8, radius = 8, sym_source = None):
      '''
 DESCRIPTION
@@ Line 105: / Line 110: @@
      The mesh will dynamically follow the center of the view.
      Contour leveo of isomesh can be changed by PageDown and PageUp keys.
-−
-     NOTE: Crystallographic operations will not be applied to the map.
+     NOTE: Crystallographic operations can be applied to the map.
 USAGE
-     dynamic_mesh mapname [, level [, radius]]
+     dynamic_mesh mapname [, level [, radius [, sym_source]]]
 ARGUMENTS
@@ Line 120: / Line 124: @@
      radius = float: radius of isomesh around the center of the view {default: 8}
-−
 SEE ALSO
      isomesh
      '''
-−
      cmd.delete("dynamic_mesh") # TODO: support multiple meshs
      cmd.delete("dymesh_callback")
-     cmd.load_callback(DynamicMesh(meshname, float(level), float(radius)),'dymesh_callback')
+     cmd.load_callback(DynamicMesh(meshname, float(level), float(radius), sym_source), 'dymesh_callback')
-−
 cmd.extend('dynamic_mesh', dynamic_mesh)
 cmd.auto_arg[0]['dynamic_mesh'] = [ cmd.map_sc, 'map object', ', ']
 </syntaxhighlight>
@@ Line 139: / Line 147: @@
 * [[get_position]]
 * [[Density Wizard]]
 * Coot http://lmb.bioch.ox.ac.uk/coot/
 [[Category:Script_Library]]
 [[Category:UI_Scripts]]