From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 3 May 2023 16:18:55 +0000 (+0100)
Subject: JAL-629 a bit more documentation
X-Git-Tag: Release_2_11_4_0~348
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b8781bdce3e54b27102f53d1e3cb5fe2c9d27b6c;p=jalview.git

JAL-629 a bit more documentation
---

diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html
index 9b1e88d..4a173d2 100644
--- a/help/help/html/features/clarguments-ng.html
+++ b/help/help/html/features/clarguments-ng.html
@@ -79,7 +79,7 @@
 
   <h3>Typical Use Cases</h3>
 
-  <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--newframe</code>)</h4>
+  <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h4>
 
   <p>
   To simply open one or more alignment files in different frames just put the filenames as the first arguments:
@@ -149,17 +149,17 @@
   <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>
+  <h5 name="--new"><code>--new</code></h5>
 
   <p>
-  To append different sets of alignment files in different frames, use <code>--newframe</code> to move on to a new alignment frame:
+  To append different sets of alignment files in different frames, use <code>--new</code> to move on to a new alignment frame:
   <pre>
-  jalview --append these/filename*.fa --newframe --append other/filename*.fa
+  jalview --append these/filename*.fa --new --append other/filename*.fa
   </pre>
   </p>
 
   <p>
-  <code>--open</code> is like using <code>--newframe --append</code> applied to every filename/URL given to <code>--open</code>
+  <code>--open</code> is like using <code>--new --append</code> applied to every filename/URL given to <code>--open</code>
   </p>
 
 
@@ -270,7 +270,7 @@
   </p>
 
   <p>
-  <code>index</code>:
+  <em><code>index</code></em>:
   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
@@ -290,7 +290,8 @@
   <code>chimerax</code>,
   <br/>
   <code>pymol</code>.
-  <br/>
+  </p>
+  <p>
   <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