Isomesh - Revision history

Cchem: 1 revision

2020-12-07T04:05:33Z

1 revision

Speleo3: better example

2020-10-01T13:38:09Z

better example

Cchem: 12 revisions

2018-04-03T18:09:01Z

12 revisions

Jaredsampson: /* USAGE */ add units for "level" parameter

2018-03-08T17:19:21Z

USAGE: add units for "level" parameter

Pyadmin: 1 revision

2014-03-28T02:16:28Z

1 revision

Speleo3: 1.7

2014-01-16T16:49:58Z

1.7

TakanoriNakane: map around the center, map extension

2012-08-25T01:34:56Z

map around the center, map extension

New page

'''isomesh''' creates a mesh isosurface object from a map object.

===USAGE===
isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]]

*name = the name for the new mesh isosurface object.
*map = the name of the map object to use for computing the mesh.
*level = the contour level.
*selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
*state = the state into which the object should be loaded (default=1) (set state=0 to append new mesh as a new state)
*carve = a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.

=== Examples ===
<source lang="python">
# load the map
load mymap.xplor, themap
# view the isomesh map
isomesh themapobject, themap, 2.0, site, carve=1.6
</source>
[[Image:Isomesh_ex1.png|thumb|right|300px|Output from the 2nd example]]
<source lang="python">
# create fake map for demo
load $TUT/1hpv.pdb

# set b and q for all atoms
alter all, b=10
alter all, q=1

# make a new map
map_new fake_map, gaussian, 0.5, all

# carved brick
isomesh carved, fake_map, 1.0, resi 200, carve=2.1

color marine, carved

# normal brick
isomesh normal, fake_map, 1.0, resi 200, 2.1

orient resi 200
</source>

===NOTES===
====USAGE====
If the mesh object already exists, then the new mesh will be appended onto the object as a new state (unless you indicate a state).

*state > 0: specific state
*state = 0: all states
*state = -1: current state

*source_state > 0: specific state
*source_state = 0: include all states starting with 0
*source_state = -1: current state
*source_state = -2: last state in map

====MAP AROUND THE CENTER====

You can create mesh around the center of the view by specifying "center" as the selection argument.

<source lang="python">
isomesh normal, fake_map, 1.0, center
</source>

====MAP OUTSIDE THE CALCULATED AREA====

When [[map_auto_expand_sym]] is ON, you can create mesh beyond the precalculated volume. In this
case, symmetry information (lattice constants, space group) of the model specified in the selection
argument, not the map object itself, is used.

====MAP LEVELS====
* Generally speaking there is some ambiguity with visualization tools as to how map data is to treated: Some map file formats are normalized by convention (in the file data itself) and others do not. Some visualization tools automatically normalize maps upon reading, others do not. PyMOL's default behavior is dependent upon map file type: CCP4 and O/BRIX/DSN6 maps are automatically normalized upon reading (disable via '''normalize_*''' settings), other maps types are not. PyMOL's normalization is a straight statistical average of all map points -- this may or may not be what you want. If migrating to PyMOL from another tool, then it is definitely worth comparing how the maps are being represented by creating an equivalent figure in both, making sure that they match, and if they do not, then figuring out why not. ''From the PyMOL list. Author: Warren DeLano.''

===SEE ALSO===
*[[isodot]]
*[[load]]
*[[fetch]]
*[[dynamic_mesh]]

[[Category:Commands|Isomesh]]
[[Category:States|Isomesh]]
[[Category:Electron_Density]]
[[Category:Maps]]

Vinnyrose at 14:08, 20 June 2009

2009-06-20T14:08:16Z

New page

===DESCRIPTION===
'''isomesh''' creates a mesh isosurface object from a map object.

===USAGE===
isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]]

*name = the name for the new mesh isosurface object.
*map = the name of the map object to use for computing the mesh.
*level = the contour level.
*selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
*state = the state into which the object should be loaded (default=1) (set state=0 to append new mesh as a new state)
*carve = a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.

=== Examples ===
<source lang="python">
# load the map
load mymap.xplor, themap
# view the isomesh map
isomesh themapobject, themap, 2.0, site, carve=1.6
</source>
[[Image:Isomesh_ex1.png|thumb|right|300px|Output from the 2nd example]]
<source lang="python">
# create fake map for demo
load $TUT/1hpv.pdb

# set b and q for all atoms
alter all, b=10
alter all, q=1

# make a new map
map_new fake_map, gaussian, 0.5, all

# carved brick
isomesh carved, fake_map, 1.0, resi 200, carve=2.1

color marine, carved

# normal brick
isomesh normal, fake_map, 1.0, resi 200, 2.1

orient resi 200
</source>

===NOTES===
====USAGE====
If the mesh object already exists, then the new mesh will be appended onto the object as a new state (unless you indicate a state).

*state > 0: specific state
*state = 0: all states
*state = -1: current state

*source_state > 0: specific state
*source_state = 0: include all states starting with 0
*source_state = -1: current state
*source_state = -2: last state in map

====MAP LEVELS====
* Generally speaking there is some ambiguity with visualization tools as to how map data is to treated: Some map file formats are normalized by convention (in the file data itself) and others do not. Some visualization tools automatically normalize maps upon reading, others do not. PyMOL's default behavior is dependent upon map file type: CCP4 and O/BRIX/DSN6 maps are automatically normalized upon reading (disable via '''normalize_*''' settings), other maps types are not. PyMOL's normalization is a straight statistical average of all map points -- this may or may not be what you want. If migrating to PyMOL from another tool, then it is definitely worth comparing how the maps are being represented by creating an equivalent figure in both, making sure that they match, and if they do not, then figuring out why not. ''From the PyMOL list. Author: Warren DeLano.''

===SEE ALSO===
[[isodot]], [[load]]

[[Category:Commands|Isomesh]]
[[Category:States|Isomesh]]

Tree at 05:56, 23 February 2005

2005-02-23T05:56:58Z

New page

===DESCRIPTION===

"isomesh" creates a mesh isosurface object from a map object.

===USAGE===

isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]]

name = the name for the new mesh isosurface object.

map = the name of the map object to use for computing the mesh.

level = the contour level.

selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided).

state = the state into which the object should be loaded (default=1)
(set state=0 to append new mesh as a new state)

carve = a radius about each atom in the selection for which to
include density. If "carve" is not provided, then the whole
brick is displayed.

===NOTES===

If the mesh object already exists, then the new mesh will be
appended onto the object as a new state (unless you indicate a state).

state > 0: specific state
state = 0: all states
state = -1: current state

source_state > 0: specific state
source_state = 0: include all states starting with 0
source_state = -1: current state
source_state = -2: last state in map

===SEE ALSO===

[[Cmd isodot]], [[Cmd load]]

[[Category:Commands|isomesh]]

← Older revision	Revision as of 04:05, 7 December 2020
(No difference)

@@ Line 1: / Line 1: @@
 '''isomesh''' creates a mesh isosurface object from a map object.
-===USAGE===
+== Usage ==
   isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]]
-*name = the name for the new mesh isosurface object.
+*name = str: the name for the new mesh isosurface object.
-*map = the name of the map object to use for computing the mesh.
+*map = str: the name of the map object to use for computing the mesh.
-*level = the contour level (in sigma units)
+*level = float: the contour level (in sigma units) {default: 1.0}
-*selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
+*selection = str: an atom selection about which to display the mesh with an additional "buffer" (if provided).
-*state = the state into which the object should be loaded (default=1) (set state=0 to append new mesh as a new state)
+*buffer = float: (see selection)
-*carve = a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.
+*state = int: the state into which the object should be loaded (default=1) (set state=0 to append new mesh as a new state) {default: 1}
-=== Examples ===
+== Example ==
 <source lang="python">
-# load the map
+fetch 6sps
-load mymap.xplor, themap
+fetch 6sps, type=2fofc
-# view the isomesh map
-isomesh themapobject, themap, 2.0, site, carve=1.6
+# mesh for entire map object
 </source>
-# set b and q for all atoms
+{|class="wikitable"
-alter all, b=10
+! mesh_all
-alter all, q=1
+! mesh_ligand
-# make a new map
+== Details ==
-# carved brick
+==== Selection Argument ====
-color marine, carved
+The arguments <code>selection</code>, <code>buffer</code> and <code>carve</code> can limit the mesh display to a selected area, and/or extend the area by symmetry operators if the selection is located outside the map bounding box itself.
-# normal brick
+[[File:isomesh-buffer-carve.png]]
-orient resi 200
+==== State Arguments ====
 If the mesh object already exists, then the new mesh will be appended onto the object as a new state (unless you indicate a state).
@@ Line 71: / Line 84: @@
 * Generally speaking there is some ambiguity with visualization tools as to how map data is to treated:  Some map file formats are normalized by convention (in the file data itself) and others do not.  Some visualization tools automatically normalize maps upon reading, others do not.  PyMOL's default behavior is dependent upon map file type: CCP4 and O/BRIX/DSN6 maps are automatically normalized upon reading (disable via '''normalize_*''' settings), other maps types are not.  PyMOL's normalization is a straight statistical average of all map points -- this may or may not be what you want.   If migrating to PyMOL from another tool, then it is definitely worth comparing how the maps are being represented by creating an equivalent figure in both, making sure that they match, and if they do not, then figuring out why not. ''From the PyMOL list.  Author: Warren DeLano.''
-===SEE ALSO===
+== See Also ==
 *[[isodot]]
 *[[load]]

← Older revision	Revision as of 18:09, 3 April 2018
(No difference)

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 66: / Line 66: @@
 When [[map_auto_expand_sym]] is ON, you can create mesh beyond the precalculated volume. In this
 case, symmetry information (lattice constants, space group) of the model specified in the selection
-argument, not the map object itself, is used.
+argument if available, or (new in 1.7) from the map object.
 ====MAP LEVELS====