Editing Isomesh (section)

== Details ==

==== Selection Argument ====

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.

[[File:isomesh-buffer-carve.png]]

==== 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).

*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 if available, or (new in 1.7) from the map object.

====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.''