Dynamic mesh

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 mapname [, level [, radius [, sym_source]]]

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}
sym_source = string: name of object from which symmetry
                 information is derived {default: None}

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.

Script

# 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', ', ']

See Also

• isomesh
• get_position
• Density Wizard
• map_auto_expand_sym
• Coot http://lmb.bioch.ox.ac.uk/coot/