File formats/Surfaces - Revision history

AngelHerraez: pmesh command deprecated, use isosurface

2012-02-29T17:20:16Z

pmesh command deprecated, use isosurface

AngelHerraez at 15:15, 21 January 2011

2011-01-21T15:15:03Z

AngelHerraez: XPLOR and CCP4 formats

2010-01-19T20:13:44Z

XPLOR and CCP4 formats

AngelHerraez: info on XML-JVXL format

2010-01-19T19:58:18Z

info on XML-JVXL format

Kmcallenberg: fixed broken link

2009-07-15T16:52:18Z

fixed broken link

AngelHerraez: fill content brought from File formats page

2009-04-25T10:54:33Z

fill content brought from File formats page

AngelHerraez: for splitting the contents of File formats page

2009-04-23T19:06:11Z

for splitting the contents of File formats page

New page

for splitting the contents of [[File formats]] page
--to be done

@@ Line 42: / Line 42: @@
 == Pmesh ==
-Jmol reads pmesh files for rendering pmesh surfaces, using not the <code>load</code> command, but the [{{ScriptingDoc}}#pmesh<code>pmesh</code> command]. (Latest 11.7.x versions integrate this into the [{{ScriptingDoc}}#isosurface<code>isosurface</code> command]).
+Jmol reads pmesh files for rendering pmesh surfaces, using not the <code>load</code> command, but the [{{ScriptingDoc}}#isosurface<code>isosurface</code> command].
 Example files [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/pmesh/ folder] and another [{{ScriptingDoc}}misc/10x10pmesh.txt example file].
 == Cube (Gaussian) ==

@@ Line 86: / Line 86: @@
 == XPLOR ==
 == CCP4 ==
-Jmol (starting versions 11.8.18 and 11.9.20) can read electron density maps in the formats XPLOR (CNS/XPLOR, Crystallography & NMR System, Yale Univ.) and CCP4 (MRC/CCP4, Medical Research Council).
+Jmol (starting versions 11.8.18 and 11.9.20) can read electron density maps in the CCP4 format (MRC/CCP4, Medical Research Council).

← Older revision		Revision as of 20:13, 19 January 2010
Line 83:		Line 83:

	The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are described together by the surface color: red --> blue colors correspond to negative --> positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residues.		The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are described together by the surface color: red --> blue colors correspond to negative --> positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residues.
		+
		+
		+	== XPLOR ==
		+	== CCP4 ==
		+
		+	Jmol (starting versions 11.8.18 and 11.9.20) can read electron density maps in the formats XPLOR (CNS/XPLOR, Crystallography & NMR System, Yale Univ.) and CCP4 (MRC/CCP4, Medical Research Council).

← Older revision		Revision as of 19:58, 19 January 2010
Line 8:		Line 8:

	Documented at {{ScriptingDoc}}misc/JVXL-format.pdf		Documented at {{ScriptingDoc}}misc/JVXL-format.pdf
		+
		+
		+	== XJVXL ==
		+	An XML-formatted variant of JVXL (used by recent versions of Jmol, post-11.9.7).
		+
		+	Latest Jmol versions implement this format by default when writing some of the
		+	newer features, such as discrete contours and the reading of [[File_formats/Surfaces#Efvet\|Efvet]]
		+	(triangle-data files). If you use
		+	set testflag4 true
		+	then it writes XML by default for any isosurface.
		+
		+	The new XML format allows for specifying everything that the original JVXL
		+	format did, but does it in a much more understandable way and will be the
		+	basis for expanded capability.
		+
		+	The basic layout is shown in [[File_formats/Sample_xjvxl\|this example]] and is just (figuratively -- all this is really XML):
		+	<pre>
		+	[header stuff]
		+	[volume data]
		+	[isosurfaceSet]
		+	[isosurface 1]
		+	[parameters and information]
		+	[surface data]
		+	[contour data]
		+	[isosurface 2]
		+	...
		+	</pre>
		+
		+	Here <code>[surface data]</code> can be any one of a number of definitions of a surface, including edges and color mapping, or of how color is mapped to a plane, or a definition of a set of triangles (not necessarily an "iso"-surface) and how they are to be colored.
		+
		+	The <code>[contour data]</code> there is somewhat new. This allows one to specify a set of lines running along the surface in any way whatsoever, but typically representing contours.

@@ Line 42: / Line 42: @@
 Documentation:
 * [{{ScriptingDoc}}misc/JVXL-format.pdf Jmol interpretation of DX files and re-exporting into much smaller JVXL files]
-* [http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format DX generation of MEP data by APBS]
+* [http://apbs.wustl.edu/MediaWiki/index.php/File_formats#OpenDX_scalar_data_format DX generation of MEP data by APBS]
 * [http://www.opendx.org OpenDX specification and software package]

← Older revision		Revision as of 10:54, 25 April 2009
Line 1:		Line 1:
−	for ~~splitting~~ the ~~contents~~ of [[~~File formats~~]] ~~page~~	+	{{File_Formats}}
−	--to ~~be done~~	+	= File Formats for Surfaces =
		+
		+	== JVXL (Jmol Voxel) ==
		+	Jmol reads and writes JVXL files.
		+
		+	This format, unique to Jmol, stores isosurface data in a highly compressed format.
		+
		+	Documented at {{ScriptingDoc}}misc/JVXL-format.pdf
		+
		+
		+	== Pmesh ==
		+	Jmol reads pmesh files for rendering pmesh surfaces, using not the <code>load</code> command, but the [{{ScriptingDoc}}#pmesh<code>pmesh</code> command]. (Latest 11.7.x versions integrate this into the [{{ScriptingDoc}}#isosurface<code>isosurface</code> command]).
		+
		+	Example files [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/pmesh/ folder] and another [{{ScriptingDoc}}misc/10x10pmesh.txt example file].
		+
		+
		+	== Cube (Gaussian) ==
		+
		+	See [[File_formats/Coordinates#Cube_(Gaussian)\|Cube]] under formats for coordinates.
		+
		+
		+	== Open DX ==
		+
		+	Jmol (11.1.18 or later) reads DX files for rendering isosurfaces and color mapping.
		+	DX contains three-dimensional scalar data; most frequently, isosurface and color by molecular electrostatic potential (MEP).
		+
		+	(Not to be confused with JCAMP-DX format, used for spectral vibrational data, which can be shown
		+	using [http://jspecview.sourceforge.net/ JSpecView Applet] and [http://www.mdlchime.com MDL Chime].)
		+
		+	Open DX files are produced, among others, by [http://apbs.sourceforge.net/ APBS] (Adaptive Poisson-Boltzmann Solver).
		+	APBS exists in standalone and web-server-based versions, and as a plug-in for [http://pymol.sourceforge.net/ PyMOL]. There is also an APBS web service integrated into [http://gemstone.mozdev.org Gemstone], which is a front-end GUI that facilitates the access to computational services run at dedicated web servers (follow the [http://gemstone.mozdev.org/usage-overview.html Gemstone tutorial]).
		+
		+	''Technical:''
		+	: DX, as Cube, defines a three-dimensional grid of points in space. At each point is a number (a "scalar value"). This set of point values is then used by Jmol to define an "isosurface" -- the surface separating points having values greater than a given cutoff from those that have a value less than a certain cutoff. A typical application is molecular orbitals. The <code>phase</code> parameter of the <code>isosurface</code> command allows bicolor rendering: one color for "points greater than x" and another color for "points less than -x".
		+	: Jmol can read DX files and re-export them to much smaller JVXL files.
		+
		+	Generally a MEP data set is not used for the isosurface itself. Rather, it is used to map color onto another isosurface, usually some representation of the "molecular surface".
		+
		+	Bottom line is that we can now take molecular electrostatic potential data that were generated in PyMOL (requires the APBS plugin for PyMOL) or in APBS or Gemstone, and use them to color a surface generated in Jmol.
		+
		+	Documentation:
		+	* [{{ScriptingDoc}}misc/JVXL-format.pdf Jmol interpretation of DX files and re-exporting into much smaller JVXL files]
		+	* [http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format DX generation of MEP data by APBS]
		+	* [http://www.opendx.org OpenDX specification and software package]
		+
		+
		+	== Efvet ==
		+
		+	Jmol (version 11.7.12 or later, support is preliminar) reads efvet files for rendering isosurfaces and color mapping.
		+	[http://ef-site.hgc.jp/eF-site/about.html Efvet format] is an XML file format used in [http://ef-site.hgc.jp/eF-site/ eF-site], a database for molecular surfaces colored by electrostatic potential, that covers the whole PDB.
		+
		+	The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are described together by the surface color: red --> blue colors correspond to negative --> positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residues.