Difference between revisions of "Dynamic mesh"

Type	Python Module
Download	dynamic_mesh.py
Author(s)	Takanori Nakane
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

Latest revision as of 01:43, 28 March 2014

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.

Note: PyMOL's Density Wizard (Menu > Wizard > Density) provides similar functionality. It is implemented using wizard framework, while this uses CallBack object.

Usage

dynamic_mesh map_name [, level [, radius [, name [ sym_source ]]]]

Arguments

map_name = string: name of volumetric object(map) to display
level = float: contour level of isomesh {default: 1.0}
radius = float: radius of isomesh around the center of the view {default: 8}
name = string: name of mesh object {default: dynamic_mesh}
sym_source = string: name of object from which symmetry information is derived {default: map_name}

Example

fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1
run dynamic_mesh.py
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.

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = module
+|filename  = dynamic_mesh.py
+|author    = [[User:TakanoriNakane|Takanori Nakane]]
+|license   = BSD-2-Clause
+}}
 '''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.
-== Script ==
-<syntaxhighlight lang="python">
-# Dynamic Mesh by Takanori Nakane, License: BSD-2 Clause
-# 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, 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, radius, sym_source):
-        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)
-        if sym_source != None:
-            cmd.set("map_auto_expand_sym", 1)
-            cmd.set_symmetry("__center__", *cmd.get_symmetry(sym_source))
-        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, sym_source = None):
-    '''
-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 can be applied to the map.
-USAGE
-    dynamic_mesh mapname [, level [, radius [, sym_source]]]
-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}
-    sym_source = string: name of object from which symmetry
-                         information is derived {default: None}
-SEE ALSO
-    isomesh
-    '''
-    cmd.delete("dynamic_mesh") # TODO: support multiple meshs
-    cmd.delete("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', ', ']
-cmd.auto_arg[3]['dynamic_mesh'] = [ cmd.object_sc, 'object', ', ']
-</syntaxhighlight>
 == See Also ==
@@ Line 152: / Line 47: @@
 [[Category:Script_Library]]
 [[Category:UI_Scripts]]
+[[Category:Pymol-script-repo]]

Difference between revisions of "Dynamic mesh"

Latest revision as of 01:43, 28 March 2014

Contents

Usage

Arguments

Example

See Also

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