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35 <div class="section" id="the-isolde-command-line">
36<h1>The ISOLDE Command Line<a class="headerlink" href="#the-isolde-command-line" title="Permalink to this headline">¶</a></h1>
37<div class="toctree-wrapper compound">
38<ul>
39<li class="toctree-l1"><a class="reference internal" href="isolde_restrain.html">Adaptive Distance Restraints</a><ul>
40<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-restrain-distances">isolde restrain distances</a></li>
41<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-restrain-single-distance">isolde restrain single distance</a></li>
42<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-release-distances">isolde release distances</a></li>
43<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-adjust-distances">isolde adjust distances</a></li>
44<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-restrain-torsions">isolde restrain torsions</a></li>
45<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-adjust-torsions">isolde adjust torsions</a></li>
46<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html#isolde-release-torsions">isolde release torsions</a></li>
47</ul>
48</li>
49<li class="toctree-l1"><a class="reference internal" href="isolde_remote.html">Remote Control Options</a><ul>
50<li class="toctree-l2"><a class="reference internal" href="isolde_remote.html#isolde-remote-rest-start">isolde remote rest start</a></li>
51<li class="toctree-l2"><a class="reference internal" href="isolde_remote.html#isolde-remote-rest-stop">isolde remote rest stop</a></li>
52<li class="toctree-l2"><a class="reference internal" href="isolde_remote.html#isolde-remote-rest-info">isolde remote rest info</a></li>
53</ul>
54</li>
55</ul>
56</div>
57<p>While the primary mode of control of ISOLDE is via <a class="reference internal" href="../tools/ISOLDE.html#isolde-gui"><span class="std std-ref">The ISOLDE GUI</span></a>, if you
58prefer you can also perform many tasks via the command line, such as launching
59the GUI (<a class="reference internal" href="#start"><span class="std std-ref">isolde start</span></a>), starting, stopping and pausing simulations (<a class="reference internal" href="#sim"><span class="std std-ref">isolde sim</span></a>),
60and performing basic manipulations (<a class="reference internal" href="#pepflip"><span class="std std-ref">isolde pepflip</span></a> and <a class="reference internal" href="#cisflip"><span class="std std-ref">isolde cisflip</span></a>). Some
61functions are currently available <em>only</em> through the command line - in
62particular, <a class="reference internal" href="isolde_restrain.html#adaptive-distance-restraints-cmd"><span class="std std-ref">Adaptive Distance Restraints</span></a>.</p>
63<div class="section" id="isolde-tutorial">
64<span id="tutorial"></span><h2>isolde tutorial<a class="headerlink" href="#isolde-tutorial" title="Permalink to this headline">¶</a></h2>
65<p>Brings up the ISOLDE <a class="reference internal" href="../tutorials/isolde.html#isolde-tutorials"><span class="std std-ref">Tutorials</span></a> help page, providing interactive
66case studies for working on models in ISOLDE.</p>
67</div>
68<div class="section" id="isolde-demo">
69<span id="demo"></span><h2>isolde demo<a class="headerlink" href="#isolde-demo" title="Permalink to this headline">¶</a></h2>
70<p>Syntax: isolde demo <em>demoName</em> [<strong>modelOnly</strong> <em>true/false</em>] [<strong>startIsolde</strong> <em>true/false</em>]</p>
71<p>Primarily intended for use with the ISOLDE tutorials. Loads saved atomic
72coordinates for use in rebuilding.</p>
73<p><em>demoName</em>: either “cryo_em” or “crystal”</p>
74<p><em>modelOnly</em>: if true, load only the model and not the electron density map</p>
75<p><em>startIsolde</em>: if true, the ISOLDE GUI will be started.</p>
76</div>
77<div class="section" id="isolde-start">
78<span id="start"></span><h2>isolde start<a class="headerlink" href="#isolde-start" title="Permalink to this headline">¶</a></h2>
79<p>Brings up <a class="reference internal" href="../tools/ISOLDE.html#isolde-gui"><span class="std std-ref">The ISOLDE GUI</span></a>. The first model in the list of open models will be
80automatically prepared with ISOLDE’s default visualisation mode. This also sets
81the display camera to orthographic projection and lighting to simple. It is
82strongly recommended that you do not change these settings during your ISOLDE
83session.</p>
84</div>
85<div class="section" id="isolde-set">
86<span id="settings"></span><h2>isolde set<a class="headerlink" href="#isolde-set" title="Permalink to this headline">¶</a></h2>
87<p>Syntax: isolde set [<strong>timeStepsPerGuiUpdate</strong> <em>integer</em>]
88[<strong>temperature</strong> <em>number</em>]</p>
89<p>Change various ISOLDE global settings.</p>
90</div>
91<div class="section" id="isolde-report">
92<span id="report"></span><h2>isolde report<a class="headerlink" href="#isolde-report" title="Permalink to this headline">¶</a></h2>
93<p>Sytax: isolde report [<strong>true|false</strong> (true)]
94[<strong>reportInterval</strong> <em>integer</em> (20)]</p>
95<p>Start/stop reporting information on simulation performance (time per coordinate
96update and timesteps per second) to the status bar. The optional
97<em>reportInterval</em> argument sets the number of coordinate updates to average over
98before reporting. Only valid while a simulation is running, and automatically
99terminates once that simulation stops.</p>
100</div>
101<div class="section" id="isolde-sim">
102<span id="sim"></span><h2>isolde sim<a class="headerlink" href="#isolde-sim" title="Permalink to this headline">¶</a></h2>
103<p>Syntax: isolde sim <em>cmd</em> [<em>atoms</em>] [<strong>discardTo</strong> <em>discardTo</em>]</p>
104<p>Start, stop or pause an interactive simulation.</p>
105<div class="section" id="isolde-sim-start-atoms">
106<h3>isolde sim start [<em>atoms</em>]<a class="headerlink" href="#isolde-sim-start-atoms" title="Permalink to this headline">¶</a></h3>
107<p>Launches the ISOLDE GUI if not already running, and starts a simulation. If no
108atoms are specified, the simulation will encompass the entirety of the current
109selected model (or the first open model if ISOLDE is not already running). If
110<em>atoms</em> is specified, the selected atoms must come from a single model
111(if this is not the current selected model, ISOLDE will automatically switch).</p>
112</div>
113<div class="section" id="isolde-sim-stop-discardto-discardto">
114<h3>isolde sim stop [<strong>discardTo</strong> <em>discardTo</em>]<a class="headerlink" href="#isolde-sim-stop-discardto-discardto" title="Permalink to this headline">¶</a></h3>
115<p><em>discardTo</em>: one of “checkpoint” or “start”</p>
116<p>Stop the currently running simulation, and optionally discard the results. If
117<em>discardTo</em> is not specified, the current state of the model will be kept.
118Otherwise, the atomic positions and states of all restraints will be reverted
119either to the starting state or the last saved checkpoint.</p>
120</div>
121<div class="section" id="isolde-sim-pause">
122<h3>isolde sim pause<a class="headerlink" href="#isolde-sim-pause" title="Permalink to this headline">¶</a></h3>
123<p>Pauses/resumes the current simulation.</p>
124</div>
125</div>
126<div class="section" id="isolde-pepflip">
127<span id="pepflip"></span><h2>isolde pepflip<a class="headerlink" href="#isolde-pepflip" title="Permalink to this headline">¶</a></h2>
128<p>Syntax: isolde pepflip <em>atoms</em></p>
129<p>Attempt to flip the peptide bond N-terminal to each selected residue, starting a
130suitable simulation if none is currently running. Requires ISOLDE to already be
131initialised. Residues outside the model currently selected for ISOLDE (or
132outside the mobile selection if a simulation is running) will not be flipped.</p>
133</div>
134<div class="section" id="isolde-cisflip">
135<span id="cisflip"></span><h2>isolde cisflip<a class="headerlink" href="#isolde-cisflip" title="Permalink to this headline">¶</a></h2>
136<p>Syntax: isolde cisflip <em>atoms</em></p>
137<p>Attempt to flip the peptide bond N-terminal to each selected residue from <em>cis</em>
138to <em>trans</em> or vice versa, starting a suitable simulation if none is currently
139running. Requires ISOLDE to already be initialised. Residues outside the model
140currently selected for ISOLDE (or outside the mobile selection if a simulation
141is running) will not be flipped.</p>
142</div>
143<div class="section" id="isolde-ignore">
144<span id="ignore"></span><h2>isolde ignore<a class="headerlink" href="#isolde-ignore" title="Permalink to this headline">¶</a></h2>
145<p>Syntax: isolde ignore <em>residues</em></p>
146<p>Tell ISOLDE to ignore a selection of residues in future simulations. This will
147not take effect until the next simulation is started. Ignored residues will
148still be used for structure factor calculations, but do not take part in
149simulations in any way. Atoms directly bonded to an ignored residue will be
150fixed in space. This command is most useful in dealing with severe clashes that
151are otherwise intractable (e.g. docked homology models with intertwined loops):</p>
152<ul class="simple">
153<li><p>select one of the clashing chains</p></li>
154<li><p><em>isolde ignore sel</em> to ignore it</p></li>
155<li><p>start a simulation and remodel its counterpart into density</p></li>
156<li><p>stop the simulation, then <em>isolde ~ignore</em> to clear the list of ignored
157residues</p></li>
158<li><p>if necessary, ignore the selection you just remodelled and run a
159simulation to fix the other side of the problem area</p></li>
160<li><p>stop any running simulation, <em>isolde ~ignore</em>, then run a final simulation
161with everything included to resolve any remaining clashes.</p></li>
162</ul>
163</div>
164<div class="section" id="id1">
165<span id="id2"></span><h2>isolde ~ignore<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
166<p>Syntax: isolde ~ignore <em>residues</em></p>
167<p>Tell ISOLDE to stop ignoring a selection of residues for simulation purposes.
168This will not take effect until the next new simulation is started.</p>
169</div>
170<div class="section" id="isolde-restrain-distances">
171<span id="restrain-distances"></span><h2>isolde restrain distances<a class="headerlink" href="#isolde-restrain-distances" title="Permalink to this headline">¶</a></h2>
172<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-distance-restraints-cmd"><span class="std std-ref">Adaptive Distance Restraints</span></a></p>
173</div>
174<div class="section" id="isolde-release-distances">
175<span id="release-distances"></span><h2>isolde release distances<a class="headerlink" href="#isolde-release-distances" title="Permalink to this headline">¶</a></h2>
176<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-distance-restraints-cmd"><span class="std std-ref">Adaptive Distance Restraints</span></a></p>
177</div>
178<div class="section" id="isolde-adjust-distances">
179<span id="adjust-distances"></span><h2>isolde adjust distances<a class="headerlink" href="#isolde-adjust-distances" title="Permalink to this headline">¶</a></h2>
180<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-distance-restraints-cmd"><span class="std std-ref">Adaptive Distance Restraints</span></a></p>
181</div>
182<div class="section" id="isolde-restrain-torsions">
183<span id="restrain-torsions"></span><h2>isolde restrain torsions<a class="headerlink" href="#isolde-restrain-torsions" title="Permalink to this headline">¶</a></h2>
184<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-dihedral-restraint-cmd"><span class="std std-ref">isolde restrain torsions</span></a></p>
185</div>
186<div class="section" id="isolde-adjust-torsions">
187<span id="adjust-torsions"></span><h2>isolde adjust torsions<a class="headerlink" href="#isolde-adjust-torsions" title="Permalink to this headline">¶</a></h2>
188<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-dihedral-restraint-cmd"><span class="std std-ref">isolde restrain torsions</span></a></p>
189</div>
190<div class="section" id="isolde-release-torsions">
191<span id="release-torsions"></span><h2>isolde release torsions<a class="headerlink" href="#isolde-release-torsions" title="Permalink to this headline">¶</a></h2>
192<p>See <a class="reference internal" href="isolde_restrain.html#adaptive-dihedral-restraint-cmd"><span class="std std-ref">isolde restrain torsions</span></a></p>
193</div>
194</div>
195
196
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198
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200 </div>
201 <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
202 <div class="sphinxsidebarwrapper">
203<h3><a href="../isolde.html">Table of Contents</a></h3>
204<ul class="current">
205<li class="toctree-l1"><a class="reference internal" href="../isolde.html">Home</a></li>
206<li class="toctree-l1"><a class="reference internal" href="../tools/ISOLDE.html">The ISOLDE GUI</a></li>
207<li class="toctree-l1 current"><a class="current reference internal" href="#">The ISOLDE Command Line</a><ul>
208<li class="toctree-l2"><a class="reference internal" href="isolde_restrain.html">Adaptive Distance Restraints</a></li>
209<li class="toctree-l2"><a class="reference internal" href="isolde_remote.html">Remote Control Options</a></li>
210<li class="toctree-l2"><a class="reference internal" href="#isolde-tutorial">isolde tutorial</a></li>
211<li class="toctree-l2"><a class="reference internal" href="#isolde-demo">isolde demo</a></li>
212<li class="toctree-l2"><a class="reference internal" href="#isolde-start">isolde start</a></li>
213<li class="toctree-l2"><a class="reference internal" href="#isolde-set">isolde set</a></li>
214<li class="toctree-l2"><a class="reference internal" href="#isolde-report">isolde report</a></li>
215<li class="toctree-l2"><a class="reference internal" href="#isolde-sim">isolde sim</a></li>
216<li class="toctree-l2"><a class="reference internal" href="#isolde-pepflip">isolde pepflip</a></li>
217<li class="toctree-l2"><a class="reference internal" href="#isolde-cisflip">isolde cisflip</a></li>
218<li class="toctree-l2"><a class="reference internal" href="#isolde-ignore">isolde ignore</a></li>
219<li class="toctree-l2"><a class="reference internal" href="#id1">isolde ~ignore</a></li>
220<li class="toctree-l2"><a class="reference internal" href="#isolde-restrain-distances">isolde restrain distances</a></li>
221<li class="toctree-l2"><a class="reference internal" href="#isolde-release-distances">isolde release distances</a></li>
222<li class="toctree-l2"><a class="reference internal" href="#isolde-adjust-distances">isolde adjust distances</a></li>
223<li class="toctree-l2"><a class="reference internal" href="#isolde-restrain-torsions">isolde restrain torsions</a></li>
224<li class="toctree-l2"><a class="reference internal" href="#isolde-adjust-torsions">isolde adjust torsions</a></li>
225<li class="toctree-l2"><a class="reference internal" href="#isolde-release-torsions">isolde release torsions</a></li>
226</ul>
227</li>
228<li class="toctree-l1"><a class="reference internal" href="../api/isolde.html">ISOLDE Python API</a></li>
229<li class="toctree-l1"><a class="reference internal" href="../tools/license.html">License</a></li>
230<li class="toctree-l1"><a class="reference internal" href="../tools/citing.html">Citing ISOLDE</a></li>
231<li class="toctree-l1"><a class="reference internal" href="../tools/contact.html">Contact Info</a></li>
232</ul>
233<div class="relations">
234<h3>Related Topics</h3>
235<ul>
236 <li><a href="../isolde.html">Documentation overview</a><ul>
237 <li>Previous: <a href="../tutorials/bulk_fitting/bulk_fitting.html" title="previous chapter">Bulk Flexible Fitting</a></li>
238 <li>Next: <a href="isolde_restrain.html" title="next chapter">Adaptive Distance Restraints</a></li>
239 </ul></li>
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