File: using-apbs.xml

package info (click to toggle)
apbs 1.0.0-2
  • links: PTS, VCS
  • area: main
  • in suites: lenny
  • size: 38,840 kB
  • ctags: 7,893
  • sloc: ansic: 44,537; xml: 21,399; sh: 20,613; fortran: 17,796; yacc: 2,922; python: 2,804; makefile: 567; lex: 294; sed: 205; java: 134; awk: 26
file content (130 lines) | stat: -rw-r--r-- 6,656 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
<chapter id="executable-sect"> <title>Using APBS</title>
	&invocation;

	&apbs-input;

	<sect1 id="other-programs"> <title>Using APBS with other programs</title>
		<para>APBS was designed to facilitate use with other programs.  This
			section outlines some of the programs with which APBS is known to
			work.  However, it is likely that applications which use APBS have been
			inadvertantly omitted from this list.  If you know of software that uses
			APBS and is not listed here, please contact Nathan Baker 
			<email>baker@biochem.wustl.edu</email>.
		</para>

		<sect2 id="web-sect"> <title>Web interfaces</title>
			<sect3> <title>Gemstone</title>
				<para>The Gemstone extension (<ulink
						url="http://gemstone.mozdev.org/">http://gemstone.mozdev.org/</ulink>)
					for the Firefox web browser provides a very easy-to-use
					interface to older versions of APBS (0.4.0) with all of the functionality of the
					command-line interface.  This extension currently uses web
					services provided by <ulink
						url="http://nbcr.net">NBCR</ulink>).
				</para>
				<para>
					The NBCR Web Services portal (<ulink url="http://ws.nbcr.net:8080/opal/GetServicesList.do">http://ws.nbcr.net:8080/opal/GetServicesList.do</ulink>) provides an off-site alternative for running computationally-expensive APBS calculations that won't fit on local resources.  This portal is currently running APBS 1.0.0.
				</para>
				<para>
					The NBCR Opal Web Services client for APBS (<ulink url="http://nbcr.net/services/#Software">http://nbcr.net/services/#Software</ulink>) provides a more basic interface which allows users to execute APBS jobs remotely via Python or build such functionality into their own software.
				</para>
			</sect3>
		</sect2>

		<sect2 id="gui-sect"> <title>Graphical user interfaces</title>
			<sect3> <title>PyMOL</title>
				<para>PyMOL (<ulink
						url="http://pymol.sourceforge.net/">http://pymol.sourceforge.net/</ulink>)
					is a molecular visualization and animation package which
					provides an interface to APBS.  The APBS plugin to PyMOL
					(developed by Michael George Lerner)  permits isocontour and
					surface map visualization of APBS results.
				</para>
			</sect3>
			<sect3> <title>VMD</title>
				<para>VMD (<ulink url="http://www.ks.uiuc.edu/Research/vmd/">http://www.ks.uiuc.edu/Research/vmd/</ulink>)
					is a molecular visualization and animation package which provides an
					interface to APBS.  It permits visualization of APBS results as isocontours, electric field lines, or on 
					biomolecular surfaces.  VMD also a graphical plugin to setup APBS calculations and execute them either
					locally or remotely via BioCoRE.  More information is available at 
					<ulink url="http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/">http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/</ulink>.
				</para>
			</sect3>
			<sect3> <title>PMV</title>
				<para>PMV 
					(<ulink url="http://www.scripps.edu/~sanner/python">http://www.scripps.edu/~sanner/python</ulink>)
					is a Python-based molecular visualization package which provides an
					interface to APBS.  It not only permits visualization of APBS results
					but it also integrates setup and executation of APBS calculations.
					The PMV/APBS interface 
					(<ulink url="http://mccammon.ucsd.edu/pmv_apbs/">http://mccammon.ucsd.edu/pmv_apbs/</ulink>)
					is under active development and future versions will offer even more
					setup, visualization, and analysis
					functionality.
				</para>
				<para>The APBS interface is distributed with recent beta versions of
					PMV, avalaible from 
					<ulink url="http://www.scripps.edu/~sanner/python">http://www.scripps.edu/~sanner/python</ulink>.
					Additional documention for using APBS with PMV is provided at 
					<ulink url="http://mccammon.ucsd.edu/~jswanson/apbsDoc/command_doc2.html">http://mccammon.ucsd.edu/~jswanson/apbsDoc/command_doc2.html</ulink>.
				</para>
			</sect3>
		</sect2>

		<sect2 id="simulation-sect"> <title>Simulation software</title>
			<para> 
				Robert Konecny (<ulink url="http://mccammon.ucsd.edu">McCammon
					Group</ulink>) has developed <ulink
					url="http://mccammon.ucsd.edu/iapbs/">iAPBS</ulink> (<ulink
					url="http://mccammon.ucsd.edu/iapbs/">http://mccammon.ucsd.edu/iapbs/</ulink>),
				an interface between APBS and the simulation packages AMBER,
				CHARMM, and NAMD.  More information is available from the iAPBS
				homepage:  <ulink
					url="http://mccammon.ucsd.edu/iapbs/">http://mccammon.ucsd.edu/iapbs/
				</ulink>.
			</para>
		</sect2>

		<sect2 id="visualization-sect"> <title>Visualization software</title>
			<para>Electrostatic potentials are commonly visualized in the context of
				biomolecular structure to better understand functional aspects of
				biological systems.  This section describes molecular graphics software
				which can display potentials and other data output from APBS.  Note
				that this set of programs also includes the <link
					linkend="gui-sect">graphical users interfaces</link> listed above.
			</para>

			<sect3> <title>Dino3D</title>
				<para>Dino3D (<ulink url="http://www.dino3d.org/">http://www.dino3d.org/</ulink>
					is a molecular graphics program which can read UHBD-format
					electrostatic data.  APBS can write multigrid results in UHBD format
					(see the <link linkend="elec-write"><command>write</command></link>
					<command>ELEC</command> command) and therefore can be used with
					Dino3D.
				</para>
			</sect3>
			<sect3> <title>MOLMOL</title>
				<para>MOLMOL (<ulink url="http://www.mol.biol.ethz.ch/wuthrich/software/molmol/">http://www.mol.biol.ethz.ch/wuthrich/software/molmol/</ulink>)
					is a molecular graphics package with an emphasis on NMR-generated
					structural data.  A program is provided with APBS (see
					<filename>tools/mesh</filename> and the
					<link linkend="conversion-sect">Data conversion tools</link> in this
					manual) which converts OpenDX data to MOLMOL format.
				</para>
			</sect3>
			<sect3> <title>OpenDX</title>
				<para>OpenDX (<ulink url="http://www.opendx.org">http://www.opendx.org</ulink>)
					is a general data visualization package which can read APBS output
					using the scripts provided in
					<filename>tools/visualization/opendx</filename> (see the discussion
					of <link linkend="viz-tools">Data visualization tools</link> in this
					manual).  However, as there is no straightforward way to
					visualizate the potential in the context of the atomic structure,
					OpenDX should not a first choice for APBS visualization.
				</para>
			</sect3>
		</sect2>

	</sect1>

</chapter>