</p>
<p>
+ Not everything that can be done with the old arguments is currently implemented in the new arguments but functionality of the new command line arguments will increase over releases. Significant new functionality, particularly allowing batch processing of files, is available in the new arguments.
+ </p>
+
+ <p>
To launch Jalview from the command line, see
<a href="commandline.html">running Jalview from the command line</a>.
</p>
</pre>
</p>
+ <p>
+ <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original frames and not append to another.
+ </p>
+
<h5 name="--newframe"><code>--newframe</code></h5>
<p>
</p>
- <h4 name="">(<code></code>)</h4>
+ <h4 name="alignmentoptions">Alignment options (<code>--colour, --wrap</code>)</h4>
+
+ <h5 name="colour"><code>--colour</code></h5>
<p>
+ You can specify a residue/base colouring for the alignment using the <code>--colour</code> option (note spelling -- Jalview is made in Scotland!):
+ <pre>
+ jalview --open examples/uniref50.fa --colour gecos-flower
+ </pre>
+ There are several colour schemes that you can use. See the <a href="../colourSchemes/index.html">page on Colour Schemes</a> for details.
+ The names to use on the command line for colour schemes are:
+ </p>
+ <p>
+ <code>clustal</code>,
+ <br/>
+ <code>blosum62</code>,
+ <br/>
+ <code>pc-identity</code>,
+ <br/>
+ <code>zappo</code>,
+ <br/>
+ <code>taylor</code>,
+ <br/>
+ <code>gecos-flower</code>,
+ <br/>
+ <code>gecos-blossom</code>,
+ <br/>
+ <code>gecos-sunset</code>,
+ <br/>
+ <code>gecos-ocean</code>,
+ <br/>
+ <code>hydrophobic</code>,
+ <br/>
+ <code>helix-propensity</code>,
+ <br/>
+ <code>strand-propensity</code>,
+ <br/>
+ <code>turn-propensity</code>,
+ <br/>
+ <code>buried-index</code>,
+ <br/>
+ <code>nucleotide</code>,
+ <br/>
+ <code>nucleotide-ambiguity</code>,
+ <br/>
+ <code>purine-pyrimidine</code>,
+ <br/>
+ <code>rna-helices</code>,
+ <br/>
+ <code>t-coffee-scores</code>,
+ <br/>
+ <code>sequence-id</code>
</p>
- <h5 name=""><code>--</code></h5>
+ <h5 name="wrap"><code>--wrap</code></h5>
+ <p>
+ An alignment should open with your usual preferences stored in the <code>.jalview_properties</code> file. To open an alignment with the sequences (definitely) wrapped, following your <code>--open</code> (or first <code>--append</code>) argument use the argument <code>--wrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --wrap
+ </pre>
+ To ensure an alignment is not wrapped use <code>--nowrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --nowrap
+ </pre>
+ </p>
+
+ <h5 name="annotations"><code>--annotations</code></h5>
<p>
+ You can specify whether the currently opened alignment frame should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>. If you don't specify then your saved preference will be used.
<pre>
+ jalview --open examples/uniref50.fa --noannotations
</pre>
</p>
+ <h5 name="title"><code>--title</code></h5>
+ <p>
+ If you would like to give the alignment frame a specific title you can do so with the <code>--title</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --title "My example alignment"
+ </pre>
+ </p>
- </table>
+ <h5 name=""><code>--structure</code></h5>
+
+ <p>
+ You can add a 3D structure file to a sequence in the current alignment frame with the <code>--structure</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ </p>
+
+
+ <p>
+ <code>seqid</code>:
+ By default this attaches to the first sequence in the alignment but most likely you will want to attach it to another sequence.
+ To do this you can specify a <em>sub-value</em> with the sequence ID, by preceding the value with square brackets and <code>seqid=SequenceId</code>
+ like this:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+
+ Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
+ </p>
+
+ <p>
+ <code>index</code>:
+ You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ </p>
+
+ <p>
+ <code>viewer</code>:
+ You can specify which structure viewer (or not) to use to open the structure using the <code>viewer</code> sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the <code>viewer</code> sub-value are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code>,
+ <br/>
+ <code>chimerax</code>,
+ <br/>
+ <code>pymol</code>.
+ <br/>
+ <code>none</code> and <code>jmol</code> will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page <a href="../features/viewingpdbs.html">Discovering and Viewing PDB and 3D-Beacons structures</a> for more details.
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,viewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ </p>
+
+
+ <h4 name="">(<code></code>)</h4>
+
+ <p>
+ </p>
+
+ <h5 name=""><code>--</code></h5>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
git://source.jalview.org / jalview.git / blobdiff