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<html>
<meta http-equiv="Pragma" content="no-cache"/>
<meta http-equiv="Cache-Control" content="no-cache"/>
<meta http-equiv="Expires" content="-1" />
<title>Web Services - Sample 01: API Documentation & Validation</title>
</head>
<body>
<ul>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<ul><li><p><font face="Courier" size="2"><b>load</b></font>
<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>enable</b></font>
<i>name, parents</i><pre><a target="result" href="/apply/pymol.cmd.enable?name=map">/apply/pymol.cmd.enable?name=map</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>disable</b></font>
<i>name</i><pre><a target="result" href="/apply/pymol.cmd.disable?name=map">/apply/pymol.cmd.disable?name=map</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get_names</b></font>
<i>type, enabled_only, selection</i><pre><a target="result" href="/apply/pymol.cmd.get_names">/apply/pymol.cmd.get_names</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.get_names?enabled_only=1">/apply/pymol.cmd.get_names?enabled_only=1</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>delete</b></font>
<i>name</i><pre><a target="result" href="/apply/pymol.cmd.delete?name=ref">/apply/pymol.cmd.delete?name=ref</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>reinitialize</b></font>
<i>what, object</i><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>color</b></font>
<i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.color?color=cyan&selection=elem c">/apply/pymol.cmd.color?color=cyan&selection=elem c</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>center</b></font>
<i>selection, state, origin, animate</i><pre><a target="result" href="/apply/pymol.cmd.center?selection=polymer and resi 61">/apply/pymol.cmd.center?selection=polymer and resi 61</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>zoom</b></font>
<i>selection, buffer, state, complete, animate</i><pre><a target="result" href="/apply/pymol.cmd.zoom?selection=byres 50/ca&animate=1">/apply/pymol.cmd.zoom?selection=byres 50/ca&animate=1</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>reset</b></font>
<i>object</i><pre><a target="result" href="/apply/pymol.cmd.reset">/apply/pymol.cmd.reset</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>clip</b></font>
<i>mode, distance, selection, state</i><pre><a target="result" href="/apply/pymol.cmd.clip?mode=slab&distance=10">/apply/pymol.cmd.clip?mode=slab&distance=10</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.clip?mode=move&distance=5">/apply/pymol.cmd.clip?mode=move&distance=5</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.clip?mode=atoms&distance=2&selection=all">/apply/pymol.cmd.clip?mode=atoms&distance=2&selection=all</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>orient</b></font>
<i>selection, state, animate</i><pre><a target="result" href="/apply/pymol.cmd.orient?selection=ref&animate=2">/apply/pymol.cmd.orient?selection=ref&animate=2</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>set_view</b></font>
<i>view, animate, quiet, hand</i><pre><a target="result" href="/apply/pymol.cmd.set_view?view=[0.578752935,0.681042910,0.448581249,-0.788007200,0.608662128,0.092595495,-0.209973529,-0.407075256,0.888932705,0.000007167,-0.000031501,-51.499031067,32.479228973,33.349739075,16.644239426,43.353927612,59.644340515,-20.000000000]&animate=2">/apply/pymol.cmd.set_view?view=[0.578752935,0.681042910,0.448581249,-0.788007200,0.608662128,0.092595495,-0.209973529,-0.407075256,0.888932705,0.000007167,-0.000031501,-51.499031067,32.479228973,33.349739075,16.644239426,43.353927612,59.644340515,-20.000000000]&animate=2</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get_view</b></font>
<i>output, quiet</i><pre><a target="result" href="/apply/pymol.cmd.get_view">/apply/pymol.cmd.get_view</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>distance</b></font>
<i>name, selection1, selection2, cutoff, mode, zoom, width, length, gap, label, quiet, reset, state</i><pre><a target="result" href="/apply/pymol.cmd.distance?name=trp2trp&selection1=/pept/E/E/TRP`4/CD2&selection2=/pept/E/E/TRP`11/CD2">/apply/pymol.cmd.distance?name=trp2trp&selection1=/pept/E/E/TRP`4/CD2&selection2=/pept/E/E/TRP`11/CD2</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.distance?name=hbonds&selection1=pept&selection2=pept&mode=2&label=0">/apply/pymol.cmd.distance?name=hbonds&selection1=pept&selection2=pept&mode=2&label=0</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.show?representation=labels&selection=hbonds">/apply/pymol.cmd.show?representation=labels&selection=hbonds</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.hide?representation=labels&selection=hbonds">/apply/pymol.cmd.hide?representation=labels&selection=hbonds</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>angle</b></font>
<i>name, selection1, selection2, selection3, mode, label, reset, zoom, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.angle?name=gly-angs&selection1=gly/&selection2=gly/&selection3=gly/&mode=1">/apply/pymol.cmd.angle?name=gly-angs&selection1=gly/&selection2=gly/&selection3=gly/&mode=1</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.zoom?selection=gly-angs&animate=1">/apply/pymol.cmd.zoom?selection=gly-angs&animate=1</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>dihedral</b></font>
<i>name, selection1, selection2, selection3, selection4, mode, label, reset, zoom, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.dihedral?name=leu-dihe&selection1=6/N&selection2=6/CA&selection3=6/C&selection4=6/O">/apply/pymol.cmd.dihedral?name=leu-dihe&selection1=6/N&selection2=6/CA&selection3=6/C&selection4=6/O</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.zoom?selection=leu-dihe&animate=1">/apply/pymol.cmd.zoom?selection=leu-dihe&animate=1</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get_distance</b></font>
<i>atom1, atom2, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.get_distance?atom1=1/CA&atom2=2/CA">/apply/pymol.cmd.get_distance?atom1=1/CA&atom2=2/CA</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get_angle</b></font>
<i>atom1, atom2, atom3, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.get_angle?atom1=1/N&atom2=1/CA&atom3=1/C">/apply/pymol.cmd.get_angle?atom1=1/N&atom2=1/CA&atom3=1/C</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get_dihedral</b></font>
<i>atom1, atom2, atom3, atom4, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.get_dihedral?atom1=1/N&atom2=1/CA&atom3=1/C&atom4=2/N">/apply/pymol.cmd.get_dihedral?atom1=1/N&atom2=1/CA&atom3=1/C&atom4=2/N</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
<ul><li><p><font face="Courier" size="2"><b>isomesh</b></font>
<i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.rock">/apply/pymol.cmd.rock</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>isolevel</b></font>
<i>name, level, state, query, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isolevel?name=mesh&level=3.0">/apply/pymol.cmd.isolevel?name=mesh&level=3.0</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.isolevel?name=mesh&level=-2.0">/apply/pymol.cmd.isolevel?name=mesh&level=-2.0</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>isosurface</b></font>
<i>name, map, level, selection, buffer, state, carve, source_state, side, mode, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isosurface?name=surf&map=map&level=5.0">/apply/pymol.cmd.isosurface?name=surf&map=map&level=5.0</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.color?color=red&selection=surf">/apply/pymol.cmd.color?color=red&selection=surf</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>show</b></font>
<i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>hide</b></font>
<i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.hide?representation=nonbonded">/apply/pymol.cmd.hide?representation=nonbonded</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>set</b></font>
<i>name, value, selection, state, updates, log, quiet</i><pre><a target="result" href="/apply/pymol.cmd.set?name=stick_radius&value=0.4">/apply/pymol.cmd.set?name=stick_radius&value=0.4</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.set?name=stick_radius&value=0.15">/apply/pymol.cmd.set?name=stick_radius&value=0.15</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>get</b></font>
<i>name, selection, state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.get?name=stick_radius">/apply/pymol.cmd.get?name=stick_radius</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>label</b></font>
<i>selection, expression, quiet</i><pre><a target="result" href="/apply/pymol.cmd.label?selection=resn sul and elem s&expression='Sulfate'">/apply/pymol.cmd.label?selection=resn sul and elem s&expression='Sulfate'</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.label?selection=name ca&expression=chain+' '+resi+' '+resn">/apply/pymol.cmd.label?selection=name ca&expression=chain+' '+resi+' '+resn</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.label?selection=visible&expression=name">/apply/pymol.cmd.label?selection=visible&expression=name</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.label?selection=all&expression=">/apply/pymol.cmd.label?selection=all&expression=</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>show_as</b></font>
<i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>draw</b></font>
<i>width, height, antialias, quiet</i><pre><a target="result" href="/apply/pymol.cmd.draw?width=1024">/apply/pymol.cmd.draw?width=1024</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>ray</b></font>
<i>width, height, antialias, angle, shift, renderer, quiet, async</i><pre><a target="result" href="/apply/pymol.cmd.ray?async=1">/apply/pymol.cmd.ray?async=1</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>select</b></font>
<i>name, selection, enable, quiet, merge, state, domain</i><pre><a target="result" href="/apply/pymol.cmd.select?name=mysel1&selection=1-2/&enable=1">/apply/pymol.cmd.select?name=mysel1&selection=1-2/&enable=1</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.show?representation=spheres&selection=mysel1">/apply/pymol.cmd.show?representation=spheres&selection=mysel1</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>origin</b></font>
<i>selection, object, position, state</i><pre><a target="result" href="/apply/pymol.cmd.origin?selection=mysel1">/apply/pymol.cmd.origin?selection=mysel1</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.turn?axis=x&angle=45">/apply/pymol.cmd.turn?axis=x&angle=45</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$TUT/1hpv.pdb">/apply/pymol.cmd.load?filename=$TUT/1hpv.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>create</b></font>
<i>name, selection, source_state, target_state, discrete, zoom, quiet, singletons, extract</i><pre><a target="result" href="/apply/pymol.cmd.create?name=chA&selection=chain A">/apply/pymol.cmd.create?name=chA&selection=chain A</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.create?name=chB&selection=chain B">/apply/pymol.cmd.create?name=chB&selection=chain B</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.delete?name=1hpv">/apply/pymol.cmd.delete?name=1hpv</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.orient">/apply/pymol.cmd.orient</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>align</b></font>
<i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset</i><pre><a target="result" href="/apply/pymol.cmd.align?mobile=chA&target=chB">/apply/pymol.cmd.align?mobile=chA&target=chB</a></pre>
</p></li>
</ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
<ul><li><p><font face="Courier" size="2"><b>super</b></font>
<i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.create?name=helix2&selection=polymer and 42-60/">/apply/pymol.cmd.create?name=helix2&selection=polymer and 42-60/</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.delete?name=ref">/apply/pymol.cmd.delete?name=ref</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.orient">/apply/pymol.cmd.orient</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.super?mobile=helix1////CA&target=helix2////CA">/apply/pymol.cmd.super?mobile=helix1////CA&target=helix2////CA</a></pre>
</p></li>
<li><p><font face="Courier" size="2"><b>window</b></font>
<i>action, x, y, width, height</i><pre><a target="result" href="/apply/pymol.cmd.window?action=position&x=200&y=300">/apply/pymol.cmd.window?action=position&x=200&y=300</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.window?action=position&x=0&y=100">/apply/pymol.cmd.window?action=position&x=0&y=100</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.window?action=size&x=600&y=600">/apply/pymol.cmd.window?action=size&x=600&y=600</a></pre>
<pre><a target="result" href="/apply/pymol.cmd.window?action=size&x=800&y=700">/apply/pymol.cmd.window?action=size&x=800&y=700</a></pre>
</p></li>
</ul></html>
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